What is the relationship between the number of interactions or MI score and the number of publications ?
Vitalii Kleshchevnikov
16 January 2017
# IntAct FTP contains the following databases = c("IntAct", "MINT", "bhf-ucl", "MPIDB", "MatrixDB",
# "HPIDb","I2D-IMEx","InnateDB-IMEx", "MolCon", "UniProt", "MBInfo")
# this will take time and data traffic ~ 2.5GB
url_intact = "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt"
filename_intact = paste0("./Data/IntAct_MITAB27_release_", format(Sys.Date(), "%m-%Y.txt"))
if(!file.exists(filename_intact)) {
downloader::download(url_intact, filename_intact)
gitignore = c(substr(filename_intact, 2, nchar(filename_intact)), readLines(".gitignore"))
write(gitignore, ".gitignore")
}
# Read all IntAct - do not attemp without 2.5 GB of free RAM
library(data.table)
all.IntAct = fread(filename_intact)##
Read 0.0% of 658369 rows
Read 10.6% of 658369 rows
Read 19.7% of 658369 rows
Read 24.3% of 658369 rows
Read 30.4% of 658369 rows
Read 42.5% of 658369 rows
Read 47.1% of 658369 rows
Read 59.2% of 658369 rows
Read 69.9% of 658369 rows
Read 82.0% of 658369 rows
Read 94.2% of 658369 rows
Read 658369 rows and 42 (of 42) columns from 2.344 GB file in 00:00:19# changing column names to data.table-compatible format
{
colnames_IntAct = colnames(all.IntAct)
colnames(all.IntAct) = gsub(" ","_",colnames(all.IntAct))
colnames(all.IntAct) = gsub("\\(|\\)","",colnames(all.IntAct))
colnames(all.IntAct) = gsub("#","",colnames(all.IntAct))
}
# cleaning Taxid "taxid:9606(human)|taxid:9606(Homo sapiens)" to 9606
{
all.IntAct[, Taxid_interactor_A := gsub("taxid:|\\(.*$","",Taxid_interactor_A)]
all.IntAct[, Taxid_interactor_B := gsub("taxid:|\\(.*$","",Taxid_interactor_B)]
all.IntAct[, Host_organisms := gsub("taxid:|\\(.*$","",Host_organisms)]
# saving identifier types and cleaning interactor ids
all.IntAct[, interactor_IDs_databases_A := gsub(":.*$","",IDs_interactor_A)]
all.IntAct[, interactor_IDs_databases_B := gsub(":.*$","",IDs_interactor_B)]
all.IntAct[, IDs_interactor_A := gsub("^.*:","",IDs_interactor_A)]
all.IntAct[, IDs_interactor_B := gsub("^.*:","",IDs_interactor_B)]
all.IntAct[, bait_prey_status_A := gsub("^.*\\(|\\)","",Experimental_roles_interactor_A)]
all.IntAct[, bait_prey_status_B := gsub("^.*\\(|\\)","",Experimental_roles_interactor_B)]
all.IntAct[, Publication_Identifiers := gsub("^.*pubmed:|\\|.*$","",Publication_Identifiers)]
all.IntAct[, Confidence_values := gsub("^intact-miscore:","",Confidence_values)]
all.IntAct[, Confidence_values := gsub("-","NA",Confidence_values)]
all.IntAct[, Confidence_values := as.numeric(Confidence_values)]
all.IntAct[, Interaction_identifiers := unlist(gsubfn::strapplyc(Interaction_identifiers,"EBI-[[:digit:]]+",simplify = T)), by = Interaction_identifiers]
}## Warning: NAs introduced by coercion## Warning in `[.data.table`(all.IntAct, , `:=`(Interaction_identifiers,
## unlist(gsubfn::strapplyc(Interaction_identifiers, : RHS 1 is length 6
## (greater than the size (1) of group 281113). The last 5 element(s) will be
## discarded.## Warning in `[.data.table`(all.IntAct, , `:=`(Interaction_identifiers,
## unlist(gsubfn::strapplyc(Interaction_identifiers, : RHS 1 is length 2
## (greater than the size (1) of group 282941). The last 1 element(s) will be
## discarded.## IDs_interactor_A IDs_interactor_B
## 1: P49418 O43426
## 2: P49418 EBI-7121639
## 3: P49418 EBI-7121654
## 4: P49418 EBI-7121715
## 5: EBI-7121765 P49418
## ---
## 658365: P45973 Q9NQS7
## 658366: Q5FBB7 P83916
## 658367: Q5FBB7 P83916
## 658368: Q9NQS7 Q96GD4
## 658369: Q9NQS7 P45973
## Alt._IDs_interactor_A
## 1: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 2: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 3: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 4: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 5: intact:MINT-8094691
## ---
## 658365: intact:EBI-78219|uniprotkb:B2R8T9
## 658366: intact:EBI-989069|intact:EBI-2555999|uniprotkb:Q5FBB4|uniprotkb:Q5FBB5|uniprotkb:Q5FBB6|uniprotkb:Q5FBB8|uniprotkb:Q8N579|uniprotkb:Q8WVL0|uniprotkb:Q9BVA8|uniprotkb:Q9H275|uniprotkb:Q588H5
## 658367: intact:EBI-989069|intact:EBI-2555999|uniprotkb:Q5FBB4|uniprotkb:Q5FBB5|uniprotkb:Q5FBB6|uniprotkb:Q5FBB8|uniprotkb:Q8N579|uniprotkb:Q8WVL0|uniprotkb:Q9BVA8|uniprotkb:Q9H275|uniprotkb:Q588H5
## 658368: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## 658369: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## Alt._IDs_interactor_B
## 1: intact:EBI-2821539|uniprotkb:O43425|uniprotkb:O94984|uniprotkb:Q4KMR1
## 2: intact:MINT-8094608
## 3: intact:MINT-8094645
## 4: intact:MINT-8094663
## 5: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## ---
## 658365: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## 658366: intact:EBI-78129|uniprotkb:P23197
## 658367: intact:EBI-78129|uniprotkb:P23197
## 658368: intact:EBI-624291|uniprotkb:O14630|uniprotkb:O60446|uniprotkb:O95083|uniprotkb:Q96DV5|uniprotkb:Q9UQ46|uniprotkb:C7G533|uniprotkb:C7G534|uniprotkb:C7G535|uniprotkb:J9JID1|uniprotkb:D3DTR4|uniprotkb:B4DNM4
## 658369: intact:EBI-78219|uniprotkb:B2R8T9
## Aliases_interactor_A
## 1: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 2: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 3: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 4: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 5: psi-mi:xrprrghal(display_short)|psi-mi:EBI-7121765(display_long)
## ---
## 658365: psi-mi:cbx5_human(display_long)|uniprotkb:CBX5(gene name)|psi-mi:CBX5(display_short)|uniprotkb:Heterochromatin protein 1 homolog alpha(gene name synonym)|uniprotkb:Antigen p25(gene name synonym)|uniprotkb:HP1A(gene name synonym)
## 658366: psi-mi:sgo1_human(display_long)|uniprotkb:SGO1(gene name)|psi-mi:SGO1(display_short)|uniprotkb:SGOL1(gene name synonym)|uniprotkb:Serologically defined breast cancer antigen NY-BR-85(gene name synonym)|uniprotkb:Shugoshin-like 1(gene name synonym)
## 658367: psi-mi:sgo1_human(display_long)|uniprotkb:SGO1(gene name)|psi-mi:SGO1(display_short)|uniprotkb:SGOL1(gene name synonym)|uniprotkb:Serologically defined breast cancer antigen NY-BR-85(gene name synonym)|uniprotkb:Shugoshin-like 1(gene name synonym)
## 658368: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## 658369: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## Aliases_interactor_B
## 1: psi-mi:synj1_human(display_long)|uniprotkb:SYNJ1(gene name)|psi-mi:SYNJ1(display_short)|uniprotkb:KIAA0910(gene name synonym)|uniprotkb:Synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1(gene name synonym)
## 2: psi-mi:vrparrvlw(display_short)|psi-mi:EBI-7121639(display_long)
## 3: psi-mi:hrpvrraap(display_short)|psi-mi:EBI-7121654(display_long)
## 4: psi-mi:vrptraada(display_short)|psi-mi:EBI-7121715(display_long)
## 5: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## ---
## 658365: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## 658366: psi-mi:cbx1_human(display_long)|uniprotkb:CBX1(gene name)|psi-mi:CBX1(display_short)|uniprotkb:CBX(gene name synonym)|uniprotkb:Heterochromatin protein 1 homolog beta(gene name synonym)|uniprotkb:Modifier 1 protein(gene name synonym)|uniprotkb:M31(gene name synonym)|uniprotkb:Heterochromatin protein p25(gene name synonym)|uniprotkb:p25beta(gene name synonym)|uniprotkb:HP1Hsbeta(gene name synonym)
## 658367: psi-mi:cbx1_human(display_long)|uniprotkb:CBX1(gene name)|psi-mi:CBX1(display_short)|uniprotkb:CBX(gene name synonym)|uniprotkb:Heterochromatin protein 1 homolog beta(gene name synonym)|uniprotkb:Modifier 1 protein(gene name synonym)|uniprotkb:M31(gene name synonym)|uniprotkb:Heterochromatin protein p25(gene name synonym)|uniprotkb:p25beta(gene name synonym)|uniprotkb:HP1Hsbeta(gene name synonym)
## 658368: psi-mi:aurkb_human(display_long)|uniprotkb:AIRK2(gene name synonym)|uniprotkb:Aurora- and IPL1-like midbody-associated protein 1(gene name synonym)|uniprotkb:Aurora/IPL1-related kinase 2(gene name synonym)|uniprotkb:STK-1(gene name synonym)|uniprotkb:Serine/threonine-protein kinase 12(gene name synonym)|uniprotkb:Serine/threonine-protein kinase 5(gene name synonym)|uniprotkb:STK1(gene name synonym)|uniprotkb:STK5(gene name synonym)|uniprotkb:Aurora 1(gene name synonym)|uniprotkb:AURKB(gene name)|psi-mi:AURKB(display_short)|uniprotkb:AIK2(gene name synonym)|uniprotkb:AIM1(gene name synonym)|uniprotkb:ARK2(gene name synonym)|uniprotkb:STK12(gene name synonym)|uniprotkb:Serine/threonine-protein kinase aurora-B(gene name synonym)
## 658369: psi-mi:cbx5_human(display_long)|uniprotkb:CBX5(gene name)|psi-mi:CBX5(display_short)|uniprotkb:Heterochromatin protein 1 homolog alpha(gene name synonym)|uniprotkb:Antigen p25(gene name synonym)|uniprotkb:HP1A(gene name synonym)
## Interaction_detection_methods
## 1: psi-mi:"MI:0084"(phage display)
## 2: psi-mi:"MI:0084"(phage display)
## 3: psi-mi:"MI:0084"(phage display)
## 4: psi-mi:"MI:0084"(phage display)
## 5: psi-mi:"MI:0084"(phage display)
## ---
## 658365: psi-mi:"MI:0416"(fluorescence microscopy)
## 658366: psi-mi:"MI:0065"(isothermal titration calorimetry)
## 658367: psi-mi:"MI:0114"(x-ray crystallography)
## 658368: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)
## 658369: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)
## Publication_1st_authors Publication_Identifiers Taxid_interactor_A
## 1: Cestra et al. (1999) 10542231 9606
## 2: Cestra et al. (1999) 10542231 9606
## 3: Cestra et al. (1999) 10542231 9606
## 4: Cestra et al. (1999) 10542231 9606
## 5: Cestra et al. (1999) 10542231 -2
## ---
## 658365: Kang et al. (2011) 21346195 9606
## 658366: Kang et al. (2011) 21346195 9606
## 658367: Kang et al. (2011) 21346195 9606
## 658368: Kang et al. (2011) 21346195 9606
## 658369: Kang et al. (2011) 21346195 9606
## Taxid_interactor_B Interaction_types
## 1: 9606 psi-mi:"MI:0407"(direct interaction)
## 2: -2 psi-mi:"MI:0407"(direct interaction)
## 3: -2 psi-mi:"MI:0407"(direct interaction)
## 4: -2 psi-mi:"MI:0407"(direct interaction)
## 5: 9606 psi-mi:"MI:0407"(direct interaction)
## ---
## 658365: 9606 psi-mi:"MI:0403"(colocalization)
## 658366: 9606 psi-mi:"MI:0407"(direct interaction)
## 658367: 9606 psi-mi:"MI:0915"(physical association)
## 658368: 9606 psi-mi:"MI:0914"(association)
## 658369: 9606 psi-mi:"MI:0914"(association)
## Source_databases Interaction_identifiers
## 1: psi-mi:"MI:0471"(MINT) EBI-7121552
## 2: psi-mi:"MI:0471"(MINT) EBI-7121634
## 3: psi-mi:"MI:0471"(MINT) EBI-7121659
## 4: psi-mi:"MI:0471"(MINT) EBI-7121710
## 5: psi-mi:"MI:0471"(MINT) EBI-7121760
## ---
## 658365: psi-mi:"MI:0486"(UniProt) EBI-12599676
## 658366: psi-mi:"MI:0486"(UniProt) EBI-12602314
## 658367: psi-mi:"MI:0486"(UniProt) EBI-12602620
## 658368: psi-mi:"MI:0486"(UniProt) EBI-12685254
## 658369: psi-mi:"MI:0486"(UniProt) EBI-12685254
## Confidence_values Expansion_methods
## 1: 0.56 -
## 2: 0.44 -
## 3: 0.44 -
## 4: 0.44 -
## 5: 0.44 -
## ---
## 658365: 0.80 -
## 658366: 0.54 -
## 658367: 0.54 -
## 658368: 0.84 psi-mi:"MI:1060"(spoke expansion)
## 658369: 0.80 psi-mi:"MI:1060"(spoke expansion)
## Biological_roles_interactor_A
## 1: psi-mi:"MI:0499"(unspecified role)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0499"(unspecified role)
## 4: psi-mi:"MI:0499"(unspecified role)
## 5: psi-mi:"MI:0499"(unspecified role)
## ---
## 658365: psi-mi:"MI:0499"(unspecified role)
## 658366: psi-mi:"MI:0499"(unspecified role)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0499"(unspecified role)
## 658369: psi-mi:"MI:0499"(unspecified role)
## Biological_roles_interactor_B
## 1: psi-mi:"MI:0499"(unspecified role)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0499"(unspecified role)
## 4: psi-mi:"MI:0499"(unspecified role)
## 5: psi-mi:"MI:0499"(unspecified role)
## ---
## 658365: psi-mi:"MI:0499"(unspecified role)
## 658366: psi-mi:"MI:0499"(unspecified role)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0499"(unspecified role)
## 658369: psi-mi:"MI:0499"(unspecified role)
## Experimental_roles_interactor_A
## 1: psi-mi:"MI:0498"(prey)
## 2: psi-mi:"MI:0498"(prey)
## 3: psi-mi:"MI:0498"(prey)
## 4: psi-mi:"MI:0498"(prey)
## 5: psi-mi:"MI:0496"(bait)
## ---
## 658365: psi-mi:"MI:0497"(neutral component)
## 658366: psi-mi:"MI:0497"(neutral component)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0496"(bait)
## 658369: psi-mi:"MI:0496"(bait)
## Experimental_roles_interactor_B Types_interactor_A
## 1: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 2: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 3: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 4: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 5: psi-mi:"MI:0498"(prey) psi-mi:"MI:0327"(peptide)
## ---
## 658365: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 658366: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 658367: psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0326"(protein)
## 658368: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 658369: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## Types_interactor_B
## 1: psi-mi:"MI:0326"(protein)
## 2: psi-mi:"MI:0327"(peptide)
## 3: psi-mi:"MI:0327"(peptide)
## 4: psi-mi:"MI:0327"(peptide)
## 5: psi-mi:"MI:0326"(protein)
## ---
## 658365: psi-mi:"MI:0326"(protein)
## 658366: psi-mi:"MI:0326"(protein)
## 658367: psi-mi:"MI:0326"(protein)
## 658368: psi-mi:"MI:0326"(protein)
## 658369: psi-mi:"MI:0326"(protein)
## Xrefs_interactor_A
## 1: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-376294(identity)
## 2: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094601(identity)
## 3: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094629(identity)
## 4: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094653(identity)
## 5: mint:MINT-8094693(identity)
## ---
## 658365: go:"GO:0000776"(kinetochore)|go:"GO:0003682"(chromatin binding)|go:"GO:0010369"(chromocenter)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0035097"(histone methyltransferase complex)|go:"GO:0031618"(nuclear pericentric heterochromatin)|go:"GO:0005635"(nuclear envelope)|go:"GO:0005730"(nucleolus)|go:"GO:0017053"(transcriptional repressor complex)|go:"GO:0007596"(blood coagulation)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|refseq:NP_001120793.1|refseq:NP_001120794.1|refseq:NP_036249.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:3FDT|rcsb pdb:3I3C|go:"GO:0016032"(viral process)|reactome:R-HSA-983231|ensembl:ENST00000209875|ensembl:ENST00000439541|ensembl:ENST00000550411|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005720"(nuclear heterochromatin)|ensembl:ENSG00000094916|ensembl:ENSP00000209875|ensembl:ENSP00000401009|ensembl:ENSP00000449207|go:"GO:0030674"(protein binding, bridging)|go:"GO:0035064"(methylated histone binding)|go:"GO:0070491"(repressing transcription factor binding)
## 658366: reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|ensembl:ENSP00000306581|ensembl:ENSP00000410458|ensembl:ENSP00000411200|ensembl:ENST00000306698|ensembl:ENST00000412997|ensembl:ENST00000452020|go:"GO:0005737"(cytoplasm)|go:"GO:0000776"(kinetochore)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0007067"(mitotic nuclear division)|rcsb pdb:4A0I|go:"GO:0005813"(centrosome)|go:"GO:0005829"(cytosol)|go:"GO:0000922"(spindle pole)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0010457"(centriole-centriole cohesion)|go:"GO:0045132"(meiotic chromosome segregation)|refseq:NP_001012409.1|refseq:NP_001012410.1|refseq:NP_001012411.1|refseq:NP_001012412.1|refseq:NP_001012413.1|refseq:NP_001186180.1|refseq:NP_001186181.1|refseq:NP_001186182.1|refseq:NP_001186183.1|refseq:NP_001186184.1|refseq:NP_001186185.1|refseq:NP_001186186.1|refseq:NP_612493.1|ensembl:ENSG00000129810|interpro:IPR011515(Shugoshin, C-terminal)|interpro:IPR011516(Shugoshin, N-terminal)|rcsb pdb:3FGA|go:"GO:0019900"(kinase binding)|ensembl:ENST00000263753|ensembl:ENST00000417364|ensembl:ENST00000419233|ensembl:ENST00000421451|ensembl:ENST00000425061|ensembl:ENST00000437051|ensembl:ENST00000442720|ensembl:ENST00000443724|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0007059"(chromosome segregation)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0000777"(condensed chromosome kinetochore)|go:"GO:0005654"(nucleoplasm)|go:"GO:0051301"(cell division)|refseq:XP_011531675.1|refseq:XP_011531677.1|refseq:XP_011531678.1|refseq:XP_011531679.1|rcsb pdb:3Q6S|ensembl:ENSP00000263753|ensembl:ENSP00000389034|ensembl:ENSP00000394613|ensembl:ENSP00000394625|ensembl:ENSP00000394957|ensembl:ENSP00000413070|ensembl:ENSP00000414129|ensembl:ENSP00000414960
## 658367: reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|ensembl:ENSP00000306581|ensembl:ENSP00000410458|ensembl:ENSP00000411200|ensembl:ENST00000306698|ensembl:ENST00000412997|ensembl:ENST00000452020|go:"GO:0005737"(cytoplasm)|go:"GO:0000776"(kinetochore)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0007067"(mitotic nuclear division)|rcsb pdb:4A0I|go:"GO:0005813"(centrosome)|go:"GO:0005829"(cytosol)|go:"GO:0000922"(spindle pole)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0010457"(centriole-centriole cohesion)|go:"GO:0045132"(meiotic chromosome segregation)|refseq:NP_001012409.1|refseq:NP_001012410.1|refseq:NP_001012411.1|refseq:NP_001012412.1|refseq:NP_001012413.1|refseq:NP_001186180.1|refseq:NP_001186181.1|refseq:NP_001186182.1|refseq:NP_001186183.1|refseq:NP_001186184.1|refseq:NP_001186185.1|refseq:NP_001186186.1|refseq:NP_612493.1|ensembl:ENSG00000129810|interpro:IPR011515(Shugoshin, C-terminal)|interpro:IPR011516(Shugoshin, N-terminal)|rcsb pdb:3FGA|go:"GO:0019900"(kinase binding)|ensembl:ENST00000263753|ensembl:ENST00000417364|ensembl:ENST00000419233|ensembl:ENST00000421451|ensembl:ENST00000425061|ensembl:ENST00000437051|ensembl:ENST00000442720|ensembl:ENST00000443724|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0007059"(chromosome segregation)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0000777"(condensed chromosome kinetochore)|go:"GO:0005654"(nucleoplasm)|go:"GO:0051301"(cell division)|refseq:XP_011531675.1|refseq:XP_011531677.1|refseq:XP_011531678.1|refseq:XP_011531679.1|rcsb pdb:3Q6S|ensembl:ENSP00000263753|ensembl:ENSP00000389034|ensembl:ENSP00000394613|ensembl:ENSP00000394625|ensembl:ENSP00000394957|ensembl:ENSP00000413070|ensembl:ENSP00000414129|ensembl:ENSP00000414960
## 658368: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## 658369: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## Xrefs_interactor_B
## 1: reactome:R-HSA-8856828|refseq:XP_016883989.1|go:"GO:0007612"(learning)|go:"GO:1904980"(positive regulation of endosome organization)|go:"GO:0005829"(cytosol)|go:"GO:0006661"(phosphatidylinositol biosynthetic process)|go:"GO:0043647"(inositol phosphate metabolic process)|go:"GO:0046856"(phosphatidylinositol dephosphorylation)|go:"GO:0006836"(neurotransmitter transport)|go:"GO:0016082"(synaptic vesicle priming)|go:"GO:0016191"(synaptic vesicle uncoating)|go:"GO:0030117"(membrane coat)|go:"GO:0034595"(phosphatidylinositol phosphate 5-phosphatase activity)|go:"GO:0046488"(phosphatidylinositol metabolic process)|go:"GO:0046855"(inositol phosphate dephosphorylation)|go:"GO:0048489"(synaptic vesicle transport)|go:"GO:0004438"(phosphatidylinositol-3-phosphatase activity)|go:"GO:0012506"(vesicle membrane)|go:"GO:0030132"(clathrin coat of coated pit)|go:"GO:0034596"(phosphatidylinositol phosphate 4-phosphatase activity)|go:"GO:0043195"(terminal bouton)|go:"GO:0043812"(phosphatidylinositol-4-phosphate phosphatase activity)|go:"GO:0043813"(phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity)|go:"GO:0052629"(phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity)|go:"GO:0052658"(inositol-1,4,5-trisphosphate 5-phosphatase activity)|go:"GO:0052659"(inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity)|go:"GO:0097060"(synaptic membrane)|reactome:R-HSA-1660499|reactome:R-HSA-1855183|reactome:R-HSA-1855204|ensembl:ENSP00000349903|go:"GO:0048488"(synaptic vesicle endocytosis)|go:"GO:0000166"(nucleotide binding)|go:"GO:0004439"(phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity)|go:"GO:0003723"(RNA binding)|refseq:NP_001153774.1|refseq:NP_001153778.1|refseq:NP_003886.3|refseq:NP_982271.2|ensembl:ENSG00000159082|interpro:IPR015047(Region of unknown function DUF1866)|interpro:IPR005135(Endonuclease/exonuclease/phosphatase)|interpro:IPR000300(Inositol polyphosphate related phosphatase)|interpro:IPR012677(Nucleotide-binding, alpha-beta plait)|interpro:IPR000504(RNA recognition motif, RNP-1)|interpro:IPR002013(Synaptojanin, N-terminal)|rcsb pdb:1W80|rcsb pdb:2DNR|rcsb pdb:2VJ0|ensembl:ENST00000357345|go:"GO:0098793"(presynapse)|mint:MINT-376287(identity)
## 2: mint:MINT-8094610(identity)
## 3: mint:MINT-8094647(identity)
## 4: mint:MINT-8094665(identity)
## 5: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094679(identity)
## ---
## 658365: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## 658366: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0001939"(female pronucleus)|go:"GO:0001940"(male pronucleus)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0010369"(chromocenter)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0000784"(nuclear chromosome, telomeric region)|ensembl:ENST00000225603|ensembl:ENST00000393408|go:"GO:0000785"(chromatin)|go:"GO:0019899"(enzyme binding)|go:"GO:1990226"(histone methyltransferase binding)|ensembl:ENSG00000108468|ensembl:ENSP00000225603|ensembl:ENSP00000377060|go:"GO:0005720"(nuclear heterochromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005819"(spindle)|go:"GO:0003682"(chromatin binding)|refseq:NP_001120700.1|refseq:NP_006798.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:2FMM|rcsb pdb:3F2U|rcsb pdb:3Q6S|rcsb pdb:5T1G
## 658367: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0001939"(female pronucleus)|go:"GO:0001940"(male pronucleus)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0010369"(chromocenter)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0000784"(nuclear chromosome, telomeric region)|ensembl:ENST00000225603|ensembl:ENST00000393408|go:"GO:0000785"(chromatin)|go:"GO:0019899"(enzyme binding)|go:"GO:1990226"(histone methyltransferase binding)|ensembl:ENSG00000108468|ensembl:ENSP00000225603|ensembl:ENSP00000377060|go:"GO:0005720"(nuclear heterochromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005819"(spindle)|go:"GO:0003682"(chromatin binding)|refseq:NP_001120700.1|refseq:NP_006798.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:2FMM|rcsb pdb:3F2U|rcsb pdb:3Q6S|rcsb pdb:5T1G
## 658368: go:"GO:0032212"(positive regulation of telomere maintenance via telomerase)|go:"GO:0051973"(positive regulation of telomerase activity)|go:"GO:1904355"(positive regulation of telomere capping)|refseq:NP_001300879.1|refseq:NP_001300880.1|refseq:NP_001300881.1|refseq:NP_001300882.1|refseq:NP_001300883.1|refseq:NP_001300884.1|go:"GO:0007568"(aging)|go:"GO:0008283"(cell proliferation)|reactome:R-HSA-4615885|go:"GO:0032091"(negative regulation of protein binding)|interpro:IPR008271(Serine/threonine protein kinase, active site)|refseq:NP_001271455.1|go:"GO:0010369"(chromocenter)|interpro:IPR030616|go:"GO:0007051"(spindle organization)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0042787"(protein ubiquitination involved in ubiquitin-dependent protein catabolic process)|go:"GO:1901796"(regulation of signal transduction by p53 class mediator)|reactome:R-HSA-6804756|go:"GO:0005876"(spindle microtubule)|go:"GO:0031616"(spindle pole centrosome)|go:"GO:0051233"(spindle midzone)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0004674"(protein serine/threonine kinase activity)|go:"GO:0005634"(nucleus)|go:"GO:0006468"(protein phosphorylation)|go:"GO:0016570"(histone modification)|go:"GO:0031577"(spindle checkpoint)|refseq:XP_011522372.1|refseq:XP_011522374.1|ensembl:ENST00000316199|ensembl:ENST00000534871|ensembl:ENST00000578549|ensembl:ENST00000585124|rcsb pdb:4AF3|go:"GO:0032133"(chromosome passenger complex)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0005829"(cytosol)|go:"GO:0005819"(spindle)|go:"GO:0005524"(ATP binding)|go:"GO:0046872"(metal ion binding)|go:"GO:0031145"(anaphase-promoting complex-dependent catabolic process)|go:"GO:0034501"(protein localization to kinetochore)|go:"GO:0051256"(mitotic spindle midzone assembly)|refseq:NP_004208.2|interpro:IPR011009(Protein kinase-like)|interpro:IPR000719(Protein kinase, core)|interpro:IPR017441(Protein kinase ATP binding, conserved site)|go:"GO:0035174"(histone serine kinase activity)|go:"GO:0043988"(histone H3-S28 phosphorylation)|interpro:IPR028772|reactome:R-HSA-174178|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0036089"(cleavage furrow formation)|go:"GO:0032467"(positive regulation of cytokinesis)|refseq:NP_001243763.1|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0002903"(negative regulation of B cell apoptotic process)|go:"GO:0034644"(cellular response to UV)|go:"GO:0030496"(midbody)|go:"GO:0004712"(protein serine/threonine/tyrosine kinase activity)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0046777"(protein autophosphorylation)|go:"GO:0051983"(regulation of chromosome segregation)|go:"GO:0016925"(protein sumoylation)|refseq:XP_016880796.1|go:"GO:0005654"(nucleoplasm)|go:"GO:0045171"(intercellular bridge)|go:"GO:0009838"(abscission)|go:"GO:0032466"(negative regulation of cytokinesis)|ensembl:ENSG00000178999|ensembl:ENSP00000313950|ensembl:ENSP00000443869|ensembl:ENSP00000462207|ensembl:ENSP00000463999
## 658369: go:"GO:0000776"(kinetochore)|go:"GO:0003682"(chromatin binding)|go:"GO:0010369"(chromocenter)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0035097"(histone methyltransferase complex)|go:"GO:0031618"(nuclear pericentric heterochromatin)|go:"GO:0005635"(nuclear envelope)|go:"GO:0005730"(nucleolus)|go:"GO:0017053"(transcriptional repressor complex)|go:"GO:0007596"(blood coagulation)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|refseq:NP_001120793.1|refseq:NP_001120794.1|refseq:NP_036249.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:3FDT|rcsb pdb:3I3C|go:"GO:0016032"(viral process)|reactome:R-HSA-983231|ensembl:ENST00000209875|ensembl:ENST00000439541|ensembl:ENST00000550411|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005720"(nuclear heterochromatin)|ensembl:ENSG00000094916|ensembl:ENSP00000209875|ensembl:ENSP00000401009|ensembl:ENSP00000449207|go:"GO:0030674"(protein binding, bridging)|go:"GO:0035064"(methylated histone binding)|go:"GO:0070491"(repressing transcription factor binding)
## Interaction_Xrefs
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 658365: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0071962"(mitotic sister chromatid cohesion, centromeric)
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Annotations_interactor_A
## 1: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms|comment:"Stoichiometry: 1.0"
## 2: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 3: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 4: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 5: comment:mint|no-uniprot-update:
## ---
## 658365: -
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Annotations_interactor_B
## 1: comment:"Stoichiometry: 1.0"
## 2: comment:mint|no-uniprot-update:
## 3: comment:mint|no-uniprot-update:
## 4: comment:mint|no-uniprot-update:
## 5: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## ---
## 658365: -
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Interaction_annotations
## 1: comment:homomint|comment:domino|comment:mint
## 2: figure legend:F1 F2|comment:domino|comment:mint
## 3: figure legend:F1 F2|comment:domino|comment:mint
## 4: figure legend:F1 F2|comment:domino|comment:mint
## 5: figure legend:F1 F2|comment:domino|comment:mint
## ---
## 658365: figure legend:1C and 2A|comment:Colocalisation was observed during both interphase and mitosis in WT and KE mutant,; however the W174A mutant localized normally to centromeres in interphase but failed to localize to centromeres in mitosis.|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658366: figure legend:4B|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658367: figure legend:Table S1|3d-resolution:1.93A|3d-r-factors:Rworking 18.9%, Rfree 23 %|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658368: figure legend:Supp 2A|agonist:"nocodazole:-a microtubule-destabilising agent increasing the proportion of mitotic cells."|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658369: figure legend:Supp 2A|agonist:"nocodazole:-a microtubule-destabilising agent increasing the proportion of mitotic cells."|full coverage:Only protein-protein interactions|curation depth:imex curation
## Host_organisms Interaction_parameters Creation_date Update_date
## 1: -1 - 2001/01/10 2014/10/16
## 2: -1 - 2001/01/10 2014/10/16
## 3: -1 - 2001/01/10 2014/10/16
## 4: -1 - 2001/01/10 2014/10/16
## 5: -1 - 2001/01/10 2014/10/16
## ---
## 658365: 9606 - 2016/11/21 2016/11/21
## 658366: -1 kd:0.18x10^-6(molar) 2016/11/21 2016/12/08
## 658367: -1 - 2016/11/21 2016/11/28
## 658368: 9606 - 2016/11/21 2016/12/08
## 658369: 9606 - 2016/11/21 2016/12/08
## Checksums_interactor_A
## 1: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 2: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 3: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 4: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 5: rogid:cilZXZ3YLDI1s7n8WNRyUE6EnJQ-2
## ---
## 658365: rogid:yNQ+OVYYyR0Ls2cp6/xzBld1hyE9606
## 658366: rogid:rTa6IoM9PWfd6qOccSMZy1o0bBU9606
## 658367: rogid:rTa6IoM9PWfd6qOccSMZy1o0bBU9606
## 658368: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## 658369: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## Checksums_interactor_B
## 1: rogid:RA73eMbCn6F7MD0ItxF/V7QbjqM9606
## 2: rogid:lPy6gBhpgvyGSYgOqeHbjcqBtMQ-2
## 3: rogid:GsDnsVmAo8ZZoKTZ4/uDb2x+h3c-2
## 4: rogid:M+f6GE3SQXrMBiIVttW1MKhz3M0-2
## 5: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## ---
## 658365: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## 658366: rogid:W2npW/vFRcuTkStKpknsAP69q6I9606
## 658367: rogid:W2npW/vFRcuTkStKpknsAP69q6I9606
## 658368: rogid:4pmZhSoAp5JmH19k2tT+w3z9Hgo9606
## 658369: rogid:yNQ+OVYYyR0Ls2cp6/xzBld1hyE9606
## Interaction_Checksums
## 1: intact-crc:F4234557A3B54840|rigid:n+UcEH4PPLkFnIyvBiXrLefK/xU
## 2: intact-crc:880913D9000BF26E|rigid:iRObbQsaUeX0PxuKeQwZ73s8iKU
## 3: intact-crc:B68245E1F0508124|rigid:SlinPP5vIczFOGZjelrO+IXJq1s
## 4: intact-crc:8F7F46DF027DF34E|rigid:uiWbDe6gaj1XcnJXNxuLLq2l/m4
## 5: intact-crc:2EF43A66D9B2D428|rigid:/ki1zA46M4Q+rHcjCcxNhhk+5Xw
## ---
## 658365: rigid:S2Pj+tiJDfK8lcndvJ4suDk6dzc
## 658366: rigid:KF/f7qCgJl3XR/i3dS9sUX4LVck
## 658367: rigid:KF/f7qCgJl3XR/i3dS9sUX4LVck
## 658368: rigid:nFnJxwm0rB490rXXUFOd8T5H8rs
## 658369: rigid:nFnJxwm0rB490rXXUFOd8T5H8rs
## Negative
## 1: false
## 2: false
## 3: false
## 4: false
## 5: false
## ---
## 658365: false
## 658366: false
## 658367: false
## 658368: false
## 658369: false
## Features_interactor_A
## 1: binding-associated region:626-695(MINT-376295)
## 2: binding-associated region:626-695(MINT-8094602)
## 3: binding-associated region:626-695(MINT-8094630)
## 4: binding-associated region:626-695(MINT-8094654)
## 5: -
## ---
## 658365: Mutation having no effect on an interaction:89-91|mutation decreasing interaction strength:174-174|green fluorescent protein tag:?-?
## 658366: sufficient binding region:448-456
## 658367: sufficient binding region:448-456
## 658368: -
## 658369: -
## Features_interactor_B
## 1: binding-associated region:1063-1070(MINT-376288)
## 2: -
## 3: -
## 4: -
## 5: binding-associated region:626-695(MINT-8094680)
## ---
## 658365: necessary binding region:125-248|mcherry fluorescent protein tag:?-?
## 658366: sufficient binding region:108..108-185..185(IPR008251)
## 658367: sufficient binding region:108..108-185..185(IPR008251)
## 658368: -
## 658369: -
## Stoichiometrys_interactor_A Stoichiometrys_interactor_B
## 1: - -
## 2: - -
## 3: - -
## 4: - -
## 5: - -
## ---
## 658365: - -
## 658366: - -
## 658367: 1 2
## 658368: - -
## 658369: - -
## Identification_method_participant_A
## 1: psi-mi:"MI:0078"(nucleotide sequence identification)
## 2: psi-mi:"MI:0078"(nucleotide sequence identification)
## 3: psi-mi:"MI:0078"(nucleotide sequence identification)
## 4: psi-mi:"MI:0078"(nucleotide sequence identification)
## 5: psi-mi:"MI:0083"(peptide synthesis)
## ---
## 658365: psi-mi:"MI:0867"(tag visualisation by fluorescence)
## 658366: psi-mi:"MI:0396"(predetermined participant)
## 658367: psi-mi:"MI:0396"(predetermined participant)
## 658368: psi-mi:"MI:0113"(western blot)
## 658369: psi-mi:"MI:0113"(western blot)
## Identification_method_participant_B
## 1: psi-mi:"MI:0078"(nucleotide sequence identification)
## 2: psi-mi:"MI:0083"(peptide synthesis)
## 3: psi-mi:"MI:0083"(peptide synthesis)
## 4: psi-mi:"MI:0083"(peptide synthesis)
## 5: psi-mi:"MI:0078"(nucleotide sequence identification)
## ---
## 658365: psi-mi:"MI:0867"(tag visualisation by fluorescence)
## 658366: psi-mi:"MI:0396"(predetermined participant)
## 658367: psi-mi:"MI:0396"(predetermined participant)
## 658368: psi-mi:"MI:0113"(western blot)
## 658369: psi-mi:"MI:0113"(western blot)
## interactor_IDs_databases_A interactor_IDs_databases_B
## 1: uniprotkb uniprotkb
## 2: uniprotkb intact
## 3: uniprotkb intact
## 4: uniprotkb intact
## 5: intact uniprotkb
## ---
## 658365: uniprotkb uniprotkb
## 658366: uniprotkb uniprotkb
## 658367: uniprotkb uniprotkb
## 658368: uniprotkb uniprotkb
## 658369: uniprotkb uniprotkb
## bait_prey_status_A bait_prey_status_B
## 1: prey bait
## 2: prey bait
## 3: prey bait
## 4: prey bait
## 5: bait prey
## ---
## 658365: neutral component neutral component
## 658366: neutral component neutral component
## 658367: unspecified role unspecified role
## 658368: bait prey
## 658369: bait prey{
SPECIES_NAME = c("Homo sapiens", "Mus musculus", "strain ATCC 204508", "strain K12", "Drosophila melanogaster", "Caenorhabditis elegans", "Arabidopsis thaliana")
SPECIES_IDs = character()
source("SPECIES_NAME_TO_ID.R")
count = 1
for(species in SPECIES_NAME) {
x = SPECIES_NAME_TO_ID(species)
SPECIES_IDs[count] = x$SPECIES_ID
count = count+1
rm(list = "x")
}
}## [1] "UP000005640 9606 HUMAN 21032 71899 93381 Homo sapiens (Human)"
## Proteome_ID SPECIES_ID
## 1 UP000005640 9606
## [1] "UP000000589 10090 MOUSE 22280 36150 58884 Mus musculus (Mouse)"
## Proteome_ID SPECIES_ID
## 1 UP000000589 10090
## [1] "UP000002311 559292 YEAST 6721 31 6760 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)"
## Proteome_ID SPECIES_ID
## 1 UP000002311 559292
## [1] "UP000000625 83333 ECOLI 4306 9 8436 Escherichia coli (strain K12)"
## [2] "UP000002185 75379 THIK1 3134 0 3172 Thiomonas intermedia (strain K12) (Thiobacillus intermedius)"
## Proteome_ID SPECIES_ID
## 1 UP000000625 83333
## [1] "UP000000803 7227 DROME 13740 9559 23492 Drosophila melanogaster (Fruit fly)"
## [2] "UP000029768 666363 DMSVA 6 0 6 Drosophila melanogaster sigma virus (isolate Drosophila/USA/AP30/2005) (DMelSV)"
## Proteome_ID SPECIES_ID
## 1 UP000000803 7227
## [1] "UP000001940 6239 CAEEL 20079 7915 33196 Caenorhabditis elegans"
## Proteome_ID SPECIES_ID
## 1 UP000001940 6239
## [1] "UP000006548 3702 ARATH 27334 6132 33604 Arabidopsis thaliana (Mouse-ear cress)"
## Proteome_ID SPECIES_ID
## 1 UP000006548 3702## Converting UniprotAC to geneID
## Converting UniprotAC isoforms to generic
{
all.IntAct[,IDs_interactor_A_isoforms := IDs_interactor_A]
all.IntAct[,IDs_interactor_B_isoforms := IDs_interactor_B]
source("isoform_id_all_remover.R")
all.IntAct[interactor_IDs_databases_A == "uniprotkb", IDs_interactor_A := isoform_id_all_remover(IDs_interactor_A)]
all.IntAct[interactor_IDs_databases_B == "uniprotkb", IDs_interactor_B := isoform_id_all_remover(IDs_interactor_B)]
}## IDs_interactor_A IDs_interactor_B
## 1: P49418 O43426
## 2: P49418 EBI-7121639
## 3: P49418 EBI-7121654
## 4: P49418 EBI-7121715
## 5: EBI-7121765 P49418
## ---
## 658365: P45973 Q9NQS7
## 658366: Q5FBB7 P83916
## 658367: Q5FBB7 P83916
## 658368: Q9NQS7 Q96GD4
## 658369: Q9NQS7 P45973
## Alt._IDs_interactor_A
## 1: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 2: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 3: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 4: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## 5: intact:MINT-8094691
## ---
## 658365: intact:EBI-78219|uniprotkb:B2R8T9
## 658366: intact:EBI-989069|intact:EBI-2555999|uniprotkb:Q5FBB4|uniprotkb:Q5FBB5|uniprotkb:Q5FBB6|uniprotkb:Q5FBB8|uniprotkb:Q8N579|uniprotkb:Q8WVL0|uniprotkb:Q9BVA8|uniprotkb:Q9H275|uniprotkb:Q588H5
## 658367: intact:EBI-989069|intact:EBI-2555999|uniprotkb:Q5FBB4|uniprotkb:Q5FBB5|uniprotkb:Q5FBB6|uniprotkb:Q5FBB8|uniprotkb:Q8N579|uniprotkb:Q8WVL0|uniprotkb:Q9BVA8|uniprotkb:Q9H275|uniprotkb:Q588H5
## 658368: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## 658369: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## Alt._IDs_interactor_B
## 1: intact:EBI-2821539|uniprotkb:O43425|uniprotkb:O94984|uniprotkb:Q4KMR1
## 2: intact:MINT-8094608
## 3: intact:MINT-8094645
## 4: intact:MINT-8094663
## 5: intact:EBI-7121510|uniprotkb:Q75MK5|uniprotkb:Q75MM3|uniprotkb:A4D1X9|intact:MINT-109264|uniprotkb:O43538|uniprotkb:A4D1X8|uniprotkb:Q75MJ8|uniprotkb:Q8N4G0
## ---
## 658365: intact:EBI-307907|uniprotkb:A8MQD2|uniprotkb:Q5Y192
## 658366: intact:EBI-78129|uniprotkb:P23197
## 658367: intact:EBI-78129|uniprotkb:P23197
## 658368: intact:EBI-624291|uniprotkb:O14630|uniprotkb:O60446|uniprotkb:O95083|uniprotkb:Q96DV5|uniprotkb:Q9UQ46|uniprotkb:C7G533|uniprotkb:C7G534|uniprotkb:C7G535|uniprotkb:J9JID1|uniprotkb:D3DTR4|uniprotkb:B4DNM4
## 658369: intact:EBI-78219|uniprotkb:B2R8T9
## Aliases_interactor_A
## 1: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 2: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 3: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 4: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## 5: psi-mi:xrprrghal(display_short)|psi-mi:EBI-7121765(display_long)
## ---
## 658365: psi-mi:cbx5_human(display_long)|uniprotkb:CBX5(gene name)|psi-mi:CBX5(display_short)|uniprotkb:Heterochromatin protein 1 homolog alpha(gene name synonym)|uniprotkb:Antigen p25(gene name synonym)|uniprotkb:HP1A(gene name synonym)
## 658366: psi-mi:sgo1_human(display_long)|uniprotkb:SGO1(gene name)|psi-mi:SGO1(display_short)|uniprotkb:SGOL1(gene name synonym)|uniprotkb:Serologically defined breast cancer antigen NY-BR-85(gene name synonym)|uniprotkb:Shugoshin-like 1(gene name synonym)
## 658367: psi-mi:sgo1_human(display_long)|uniprotkb:SGO1(gene name)|psi-mi:SGO1(display_short)|uniprotkb:SGOL1(gene name synonym)|uniprotkb:Serologically defined breast cancer antigen NY-BR-85(gene name synonym)|uniprotkb:Shugoshin-like 1(gene name synonym)
## 658368: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## 658369: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## Aliases_interactor_B
## 1: psi-mi:synj1_human(display_long)|uniprotkb:SYNJ1(gene name)|psi-mi:SYNJ1(display_short)|uniprotkb:KIAA0910(gene name synonym)|uniprotkb:Synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1(gene name synonym)
## 2: psi-mi:vrparrvlw(display_short)|psi-mi:EBI-7121639(display_long)
## 3: psi-mi:hrpvrraap(display_short)|psi-mi:EBI-7121654(display_long)
## 4: psi-mi:vrptraada(display_short)|psi-mi:EBI-7121715(display_long)
## 5: psi-mi:amph_human(display_long)|uniprotkb:AMPH(gene name)|psi-mi:AMPH(display_short)|uniprotkb:AMPH1(gene name synonym)
## ---
## 658365: psi-mi:ince_human(display_long)|uniprotkb:INCENP(gene name)|psi-mi:INCENP(display_short)
## 658366: psi-mi:cbx1_human(display_long)|uniprotkb:CBX1(gene name)|psi-mi:CBX1(display_short)|uniprotkb:CBX(gene name synonym)|uniprotkb:Heterochromatin protein 1 homolog beta(gene name synonym)|uniprotkb:Modifier 1 protein(gene name synonym)|uniprotkb:M31(gene name synonym)|uniprotkb:Heterochromatin protein p25(gene name synonym)|uniprotkb:p25beta(gene name synonym)|uniprotkb:HP1Hsbeta(gene name synonym)
## 658367: psi-mi:cbx1_human(display_long)|uniprotkb:CBX1(gene name)|psi-mi:CBX1(display_short)|uniprotkb:CBX(gene name synonym)|uniprotkb:Heterochromatin protein 1 homolog beta(gene name synonym)|uniprotkb:Modifier 1 protein(gene name synonym)|uniprotkb:M31(gene name synonym)|uniprotkb:Heterochromatin protein p25(gene name synonym)|uniprotkb:p25beta(gene name synonym)|uniprotkb:HP1Hsbeta(gene name synonym)
## 658368: psi-mi:aurkb_human(display_long)|uniprotkb:AIRK2(gene name synonym)|uniprotkb:Aurora- and IPL1-like midbody-associated protein 1(gene name synonym)|uniprotkb:Aurora/IPL1-related kinase 2(gene name synonym)|uniprotkb:STK-1(gene name synonym)|uniprotkb:Serine/threonine-protein kinase 12(gene name synonym)|uniprotkb:Serine/threonine-protein kinase 5(gene name synonym)|uniprotkb:STK1(gene name synonym)|uniprotkb:STK5(gene name synonym)|uniprotkb:Aurora 1(gene name synonym)|uniprotkb:AURKB(gene name)|psi-mi:AURKB(display_short)|uniprotkb:AIK2(gene name synonym)|uniprotkb:AIM1(gene name synonym)|uniprotkb:ARK2(gene name synonym)|uniprotkb:STK12(gene name synonym)|uniprotkb:Serine/threonine-protein kinase aurora-B(gene name synonym)
## 658369: psi-mi:cbx5_human(display_long)|uniprotkb:CBX5(gene name)|psi-mi:CBX5(display_short)|uniprotkb:Heterochromatin protein 1 homolog alpha(gene name synonym)|uniprotkb:Antigen p25(gene name synonym)|uniprotkb:HP1A(gene name synonym)
## Interaction_detection_methods
## 1: psi-mi:"MI:0084"(phage display)
## 2: psi-mi:"MI:0084"(phage display)
## 3: psi-mi:"MI:0084"(phage display)
## 4: psi-mi:"MI:0084"(phage display)
## 5: psi-mi:"MI:0084"(phage display)
## ---
## 658365: psi-mi:"MI:0416"(fluorescence microscopy)
## 658366: psi-mi:"MI:0065"(isothermal titration calorimetry)
## 658367: psi-mi:"MI:0114"(x-ray crystallography)
## 658368: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)
## 658369: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)
## Publication_1st_authors Publication_Identifiers Taxid_interactor_A
## 1: Cestra et al. (1999) 10542231 9606
## 2: Cestra et al. (1999) 10542231 9606
## 3: Cestra et al. (1999) 10542231 9606
## 4: Cestra et al. (1999) 10542231 9606
## 5: Cestra et al. (1999) 10542231 -2
## ---
## 658365: Kang et al. (2011) 21346195 9606
## 658366: Kang et al. (2011) 21346195 9606
## 658367: Kang et al. (2011) 21346195 9606
## 658368: Kang et al. (2011) 21346195 9606
## 658369: Kang et al. (2011) 21346195 9606
## Taxid_interactor_B Interaction_types
## 1: 9606 psi-mi:"MI:0407"(direct interaction)
## 2: -2 psi-mi:"MI:0407"(direct interaction)
## 3: -2 psi-mi:"MI:0407"(direct interaction)
## 4: -2 psi-mi:"MI:0407"(direct interaction)
## 5: 9606 psi-mi:"MI:0407"(direct interaction)
## ---
## 658365: 9606 psi-mi:"MI:0403"(colocalization)
## 658366: 9606 psi-mi:"MI:0407"(direct interaction)
## 658367: 9606 psi-mi:"MI:0915"(physical association)
## 658368: 9606 psi-mi:"MI:0914"(association)
## 658369: 9606 psi-mi:"MI:0914"(association)
## Source_databases Interaction_identifiers
## 1: psi-mi:"MI:0471"(MINT) EBI-7121552
## 2: psi-mi:"MI:0471"(MINT) EBI-7121634
## 3: psi-mi:"MI:0471"(MINT) EBI-7121659
## 4: psi-mi:"MI:0471"(MINT) EBI-7121710
## 5: psi-mi:"MI:0471"(MINT) EBI-7121760
## ---
## 658365: psi-mi:"MI:0486"(UniProt) EBI-12599676
## 658366: psi-mi:"MI:0486"(UniProt) EBI-12602314
## 658367: psi-mi:"MI:0486"(UniProt) EBI-12602620
## 658368: psi-mi:"MI:0486"(UniProt) EBI-12685254
## 658369: psi-mi:"MI:0486"(UniProt) EBI-12685254
## Confidence_values Expansion_methods
## 1: 0.56 -
## 2: 0.44 -
## 3: 0.44 -
## 4: 0.44 -
## 5: 0.44 -
## ---
## 658365: 0.80 -
## 658366: 0.54 -
## 658367: 0.54 -
## 658368: 0.84 psi-mi:"MI:1060"(spoke expansion)
## 658369: 0.80 psi-mi:"MI:1060"(spoke expansion)
## Biological_roles_interactor_A
## 1: psi-mi:"MI:0499"(unspecified role)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0499"(unspecified role)
## 4: psi-mi:"MI:0499"(unspecified role)
## 5: psi-mi:"MI:0499"(unspecified role)
## ---
## 658365: psi-mi:"MI:0499"(unspecified role)
## 658366: psi-mi:"MI:0499"(unspecified role)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0499"(unspecified role)
## 658369: psi-mi:"MI:0499"(unspecified role)
## Biological_roles_interactor_B
## 1: psi-mi:"MI:0499"(unspecified role)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0499"(unspecified role)
## 4: psi-mi:"MI:0499"(unspecified role)
## 5: psi-mi:"MI:0499"(unspecified role)
## ---
## 658365: psi-mi:"MI:0499"(unspecified role)
## 658366: psi-mi:"MI:0499"(unspecified role)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0499"(unspecified role)
## 658369: psi-mi:"MI:0499"(unspecified role)
## Experimental_roles_interactor_A
## 1: psi-mi:"MI:0498"(prey)
## 2: psi-mi:"MI:0498"(prey)
## 3: psi-mi:"MI:0498"(prey)
## 4: psi-mi:"MI:0498"(prey)
## 5: psi-mi:"MI:0496"(bait)
## ---
## 658365: psi-mi:"MI:0497"(neutral component)
## 658366: psi-mi:"MI:0497"(neutral component)
## 658367: psi-mi:"MI:0499"(unspecified role)
## 658368: psi-mi:"MI:0496"(bait)
## 658369: psi-mi:"MI:0496"(bait)
## Experimental_roles_interactor_B Types_interactor_A
## 1: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 2: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 3: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 4: psi-mi:"MI:0496"(bait) psi-mi:"MI:0326"(protein)
## 5: psi-mi:"MI:0498"(prey) psi-mi:"MI:0327"(peptide)
## ---
## 658365: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 658366: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 658367: psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0326"(protein)
## 658368: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 658369: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## Types_interactor_B
## 1: psi-mi:"MI:0326"(protein)
## 2: psi-mi:"MI:0327"(peptide)
## 3: psi-mi:"MI:0327"(peptide)
## 4: psi-mi:"MI:0327"(peptide)
## 5: psi-mi:"MI:0326"(protein)
## ---
## 658365: psi-mi:"MI:0326"(protein)
## 658366: psi-mi:"MI:0326"(protein)
## 658367: psi-mi:"MI:0326"(protein)
## 658368: psi-mi:"MI:0326"(protein)
## 658369: psi-mi:"MI:0326"(protein)
## Xrefs_interactor_A
## 1: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-376294(identity)
## 2: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094601(identity)
## 3: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094629(identity)
## 4: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094653(identity)
## 5: mint:MINT-8094693(identity)
## ---
## 658365: go:"GO:0000776"(kinetochore)|go:"GO:0003682"(chromatin binding)|go:"GO:0010369"(chromocenter)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0035097"(histone methyltransferase complex)|go:"GO:0031618"(nuclear pericentric heterochromatin)|go:"GO:0005635"(nuclear envelope)|go:"GO:0005730"(nucleolus)|go:"GO:0017053"(transcriptional repressor complex)|go:"GO:0007596"(blood coagulation)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|refseq:NP_001120793.1|refseq:NP_001120794.1|refseq:NP_036249.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:3FDT|rcsb pdb:3I3C|go:"GO:0016032"(viral process)|reactome:R-HSA-983231|ensembl:ENST00000209875|ensembl:ENST00000439541|ensembl:ENST00000550411|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005720"(nuclear heterochromatin)|ensembl:ENSG00000094916|ensembl:ENSP00000209875|ensembl:ENSP00000401009|ensembl:ENSP00000449207|go:"GO:0030674"(protein binding, bridging)|go:"GO:0035064"(methylated histone binding)|go:"GO:0070491"(repressing transcription factor binding)
## 658366: reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|ensembl:ENSP00000306581|ensembl:ENSP00000410458|ensembl:ENSP00000411200|ensembl:ENST00000306698|ensembl:ENST00000412997|ensembl:ENST00000452020|go:"GO:0005737"(cytoplasm)|go:"GO:0000776"(kinetochore)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0007067"(mitotic nuclear division)|rcsb pdb:4A0I|go:"GO:0005813"(centrosome)|go:"GO:0005829"(cytosol)|go:"GO:0000922"(spindle pole)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0010457"(centriole-centriole cohesion)|go:"GO:0045132"(meiotic chromosome segregation)|refseq:NP_001012409.1|refseq:NP_001012410.1|refseq:NP_001012411.1|refseq:NP_001012412.1|refseq:NP_001012413.1|refseq:NP_001186180.1|refseq:NP_001186181.1|refseq:NP_001186182.1|refseq:NP_001186183.1|refseq:NP_001186184.1|refseq:NP_001186185.1|refseq:NP_001186186.1|refseq:NP_612493.1|ensembl:ENSG00000129810|interpro:IPR011515(Shugoshin, C-terminal)|interpro:IPR011516(Shugoshin, N-terminal)|rcsb pdb:3FGA|go:"GO:0019900"(kinase binding)|ensembl:ENST00000263753|ensembl:ENST00000417364|ensembl:ENST00000419233|ensembl:ENST00000421451|ensembl:ENST00000425061|ensembl:ENST00000437051|ensembl:ENST00000442720|ensembl:ENST00000443724|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0007059"(chromosome segregation)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0000777"(condensed chromosome kinetochore)|go:"GO:0005654"(nucleoplasm)|go:"GO:0051301"(cell division)|refseq:XP_011531675.1|refseq:XP_011531677.1|refseq:XP_011531678.1|refseq:XP_011531679.1|rcsb pdb:3Q6S|ensembl:ENSP00000263753|ensembl:ENSP00000389034|ensembl:ENSP00000394613|ensembl:ENSP00000394625|ensembl:ENSP00000394957|ensembl:ENSP00000413070|ensembl:ENSP00000414129|ensembl:ENSP00000414960
## 658367: reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|ensembl:ENSP00000306581|ensembl:ENSP00000410458|ensembl:ENSP00000411200|ensembl:ENST00000306698|ensembl:ENST00000412997|ensembl:ENST00000452020|go:"GO:0005737"(cytoplasm)|go:"GO:0000776"(kinetochore)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0007067"(mitotic nuclear division)|rcsb pdb:4A0I|go:"GO:0005813"(centrosome)|go:"GO:0005829"(cytosol)|go:"GO:0000922"(spindle pole)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0010457"(centriole-centriole cohesion)|go:"GO:0045132"(meiotic chromosome segregation)|refseq:NP_001012409.1|refseq:NP_001012410.1|refseq:NP_001012411.1|refseq:NP_001012412.1|refseq:NP_001012413.1|refseq:NP_001186180.1|refseq:NP_001186181.1|refseq:NP_001186182.1|refseq:NP_001186183.1|refseq:NP_001186184.1|refseq:NP_001186185.1|refseq:NP_001186186.1|refseq:NP_612493.1|ensembl:ENSG00000129810|interpro:IPR011515(Shugoshin, C-terminal)|interpro:IPR011516(Shugoshin, N-terminal)|rcsb pdb:3FGA|go:"GO:0019900"(kinase binding)|ensembl:ENST00000263753|ensembl:ENST00000417364|ensembl:ENST00000419233|ensembl:ENST00000421451|ensembl:ENST00000425061|ensembl:ENST00000437051|ensembl:ENST00000442720|ensembl:ENST00000443724|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0007059"(chromosome segregation)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0000777"(condensed chromosome kinetochore)|go:"GO:0005654"(nucleoplasm)|go:"GO:0051301"(cell division)|refseq:XP_011531675.1|refseq:XP_011531677.1|refseq:XP_011531678.1|refseq:XP_011531679.1|rcsb pdb:3Q6S|ensembl:ENSP00000263753|ensembl:ENSP00000389034|ensembl:ENSP00000394613|ensembl:ENSP00000394625|ensembl:ENSP00000394957|ensembl:ENSP00000413070|ensembl:ENSP00000414129|ensembl:ENSP00000414960
## 658368: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## 658369: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## Xrefs_interactor_B
## 1: reactome:R-HSA-8856828|refseq:XP_016883989.1|go:"GO:0007612"(learning)|go:"GO:1904980"(positive regulation of endosome organization)|go:"GO:0005829"(cytosol)|go:"GO:0006661"(phosphatidylinositol biosynthetic process)|go:"GO:0043647"(inositol phosphate metabolic process)|go:"GO:0046856"(phosphatidylinositol dephosphorylation)|go:"GO:0006836"(neurotransmitter transport)|go:"GO:0016082"(synaptic vesicle priming)|go:"GO:0016191"(synaptic vesicle uncoating)|go:"GO:0030117"(membrane coat)|go:"GO:0034595"(phosphatidylinositol phosphate 5-phosphatase activity)|go:"GO:0046488"(phosphatidylinositol metabolic process)|go:"GO:0046855"(inositol phosphate dephosphorylation)|go:"GO:0048489"(synaptic vesicle transport)|go:"GO:0004438"(phosphatidylinositol-3-phosphatase activity)|go:"GO:0012506"(vesicle membrane)|go:"GO:0030132"(clathrin coat of coated pit)|go:"GO:0034596"(phosphatidylinositol phosphate 4-phosphatase activity)|go:"GO:0043195"(terminal bouton)|go:"GO:0043812"(phosphatidylinositol-4-phosphate phosphatase activity)|go:"GO:0043813"(phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity)|go:"GO:0052629"(phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity)|go:"GO:0052658"(inositol-1,4,5-trisphosphate 5-phosphatase activity)|go:"GO:0052659"(inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity)|go:"GO:0097060"(synaptic membrane)|reactome:R-HSA-1660499|reactome:R-HSA-1855183|reactome:R-HSA-1855204|ensembl:ENSP00000349903|go:"GO:0048488"(synaptic vesicle endocytosis)|go:"GO:0000166"(nucleotide binding)|go:"GO:0004439"(phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity)|go:"GO:0003723"(RNA binding)|refseq:NP_001153774.1|refseq:NP_001153778.1|refseq:NP_003886.3|refseq:NP_982271.2|ensembl:ENSG00000159082|interpro:IPR015047(Region of unknown function DUF1866)|interpro:IPR005135(Endonuclease/exonuclease/phosphatase)|interpro:IPR000300(Inositol polyphosphate related phosphatase)|interpro:IPR012677(Nucleotide-binding, alpha-beta plait)|interpro:IPR000504(RNA recognition motif, RNP-1)|interpro:IPR002013(Synaptojanin, N-terminal)|rcsb pdb:1W80|rcsb pdb:2DNR|rcsb pdb:2VJ0|ensembl:ENST00000357345|go:"GO:0098793"(presynapse)|mint:MINT-376287(identity)
## 2: mint:MINT-8094610(identity)
## 3: mint:MINT-8094647(identity)
## 4: mint:MINT-8094665(identity)
## 5: go:"GO:0015629"(actin cytoskeleton)|refseq:NP_001626.1|interpro:IPR003005(Amphiphysin)|rcsb pdb:4ATM|go:"GO:0007268"(chemical synaptic transmission)|interpro:IPR003017(Amphiphysin, isoform 1)|refseq:NP_647477.1|rcsb pdb:3SOG|rcsb pdb:1UTC|interpro:IPR001452(Src homology-3)|rcsb pdb:1KY7|interpro:IPR004148(BAR)|go:"GO:0008021"(synaptic vesicle)|go:"GO:0006897"(endocytosis)|go:"GO:0030054"(cell junction)|interpro:IPR027267|go:"GO:0030672"(synaptic vesicle membrane)|go:"GO:0005086"(ARF guanyl-nucleotide exchange factor activity)|go:"GO:0005802"(trans-Golgi network)|reactome:R-HSA-8856828|ensembl:ENST00000325590|ensembl:ENST00000356264|ensembl:ENSG00000078053|ensembl:ENSP00000317441|ensembl:ENSP00000348602|go:"GO:0005543"(phospholipid binding)|go:"GO:0031256"(leading edge membrane)|mint:MINT-8094679(identity)
## ---
## 658365: rcsb pdb:4AF3|go:"GO:0000776"(kinetochore)|go:"GO:0000801"(central element)|go:"GO:0030496"(midbody)|go:"GO:0000800"(lateral element)|go:"GO:0010369"(chromocenter)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0005819"(spindle)|go:"GO:0007059"(chromosome segregation)|go:"GO:0000910"(cytokinesis)|refseq:NP_001035784.1|refseq:NP_064623.2|interpro:IPR022006|interpro:IPR005635(Inner centromere protein, ARK binding region)|rcsb pdb:2QFA|go:"GO:0000777"(condensed chromosome kinetochore)|ensembl:ENST00000278849|ensembl:ENST00000394818|go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0043234"(protein complex)|go:"GO:0007062"(sister chromatid cohesion)|ensembl:ENSG00000149503|ensembl:ENSP00000278849|ensembl:ENSP00000378295|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0007067"(mitotic nuclear division)|reactome:R-HSA-4615885|go:"GO:0005654"(nucleoplasm)|go:"GO:0016925"(protein sumoylation)
## 658366: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0001939"(female pronucleus)|go:"GO:0001940"(male pronucleus)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0010369"(chromocenter)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0000784"(nuclear chromosome, telomeric region)|ensembl:ENST00000225603|ensembl:ENST00000393408|go:"GO:0000785"(chromatin)|go:"GO:0019899"(enzyme binding)|go:"GO:1990226"(histone methyltransferase binding)|ensembl:ENSG00000108468|ensembl:ENSP00000225603|ensembl:ENSP00000377060|go:"GO:0005720"(nuclear heterochromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005819"(spindle)|go:"GO:0003682"(chromatin binding)|refseq:NP_001120700.1|refseq:NP_006798.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:2FMM|rcsb pdb:3F2U|rcsb pdb:3Q6S|rcsb pdb:5T1G
## 658367: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0001939"(female pronucleus)|go:"GO:0001940"(male pronucleus)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0010369"(chromocenter)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0000784"(nuclear chromosome, telomeric region)|ensembl:ENST00000225603|ensembl:ENST00000393408|go:"GO:0000785"(chromatin)|go:"GO:0019899"(enzyme binding)|go:"GO:1990226"(histone methyltransferase binding)|ensembl:ENSG00000108468|ensembl:ENSP00000225603|ensembl:ENSP00000377060|go:"GO:0005720"(nuclear heterochromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005819"(spindle)|go:"GO:0003682"(chromatin binding)|refseq:NP_001120700.1|refseq:NP_006798.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:2FMM|rcsb pdb:3F2U|rcsb pdb:3Q6S|rcsb pdb:5T1G
## 658368: go:"GO:0032212"(positive regulation of telomere maintenance via telomerase)|go:"GO:0051973"(positive regulation of telomerase activity)|go:"GO:1904355"(positive regulation of telomere capping)|refseq:NP_001300879.1|refseq:NP_001300880.1|refseq:NP_001300881.1|refseq:NP_001300882.1|refseq:NP_001300883.1|refseq:NP_001300884.1|go:"GO:0007568"(aging)|go:"GO:0008283"(cell proliferation)|reactome:R-HSA-4615885|go:"GO:0032091"(negative regulation of protein binding)|interpro:IPR008271(Serine/threonine protein kinase, active site)|refseq:NP_001271455.1|go:"GO:0010369"(chromocenter)|interpro:IPR030616|go:"GO:0007051"(spindle organization)|go:"GO:0007062"(sister chromatid cohesion)|go:"GO:0042787"(protein ubiquitination involved in ubiquitin-dependent protein catabolic process)|go:"GO:1901796"(regulation of signal transduction by p53 class mediator)|reactome:R-HSA-6804756|go:"GO:0005876"(spindle microtubule)|go:"GO:0031616"(spindle pole centrosome)|go:"GO:0051233"(spindle midzone)|go:"GO:0000779"(condensed chromosome, centromeric region)|go:"GO:0004674"(protein serine/threonine kinase activity)|go:"GO:0005634"(nucleus)|go:"GO:0006468"(protein phosphorylation)|go:"GO:0016570"(histone modification)|go:"GO:0031577"(spindle checkpoint)|refseq:XP_011522372.1|refseq:XP_011522374.1|ensembl:ENST00000316199|ensembl:ENST00000534871|ensembl:ENST00000578549|ensembl:ENST00000585124|rcsb pdb:4AF3|go:"GO:0032133"(chromosome passenger complex)|go:"GO:0000780"(condensed nuclear chromosome, centromeric region)|go:"GO:0005829"(cytosol)|go:"GO:0005819"(spindle)|go:"GO:0005524"(ATP binding)|go:"GO:0046872"(metal ion binding)|go:"GO:0031145"(anaphase-promoting complex-dependent catabolic process)|go:"GO:0034501"(protein localization to kinetochore)|go:"GO:0051256"(mitotic spindle midzone assembly)|refseq:NP_004208.2|interpro:IPR011009(Protein kinase-like)|interpro:IPR000719(Protein kinase, core)|interpro:IPR017441(Protein kinase ATP binding, conserved site)|go:"GO:0035174"(histone serine kinase activity)|go:"GO:0043988"(histone H3-S28 phosphorylation)|interpro:IPR028772|reactome:R-HSA-174178|reactome:R-HSA-2467813|reactome:R-HSA-2500257|reactome:R-HSA-5663220|reactome:R-HSA-68877|go:"GO:0036089"(cleavage furrow formation)|go:"GO:0032467"(positive regulation of cytokinesis)|refseq:NP_001243763.1|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0002903"(negative regulation of B cell apoptotic process)|go:"GO:0034644"(cellular response to UV)|go:"GO:0030496"(midbody)|go:"GO:0004712"(protein serine/threonine/tyrosine kinase activity)|go:"GO:0008608"(attachment of spindle microtubules to kinetochore)|go:"GO:0046777"(protein autophosphorylation)|go:"GO:0051983"(regulation of chromosome segregation)|go:"GO:0016925"(protein sumoylation)|refseq:XP_016880796.1|go:"GO:0005654"(nucleoplasm)|go:"GO:0045171"(intercellular bridge)|go:"GO:0009838"(abscission)|go:"GO:0032466"(negative regulation of cytokinesis)|ensembl:ENSG00000178999|ensembl:ENSP00000313950|ensembl:ENSP00000443869|ensembl:ENSP00000462207|ensembl:ENSP00000463999
## 658369: go:"GO:0000776"(kinetochore)|go:"GO:0003682"(chromatin binding)|go:"GO:0010369"(chromocenter)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0005721"(pericentric heterochromatin)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0035097"(histone methyltransferase complex)|go:"GO:0031618"(nuclear pericentric heterochromatin)|go:"GO:0005635"(nuclear envelope)|go:"GO:0005730"(nucleolus)|go:"GO:0017053"(transcriptional repressor complex)|go:"GO:0007596"(blood coagulation)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|refseq:NP_001120793.1|refseq:NP_001120794.1|refseq:NP_036249.1|interpro:IPR017984|interpro:IPR023780|interpro:IPR000953(Chromo domain)|interpro:IPR008251(Chromo shadow)|interpro:IPR016197(Chromo domain-like)|interpro:IPR023779|rcsb pdb:3FDT|rcsb pdb:3I3C|go:"GO:0016032"(viral process)|reactome:R-HSA-983231|ensembl:ENST00000209875|ensembl:ENST00000439541|ensembl:ENST00000550411|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005720"(nuclear heterochromatin)|ensembl:ENSG00000094916|ensembl:ENSP00000209875|ensembl:ENSP00000401009|ensembl:ENSP00000449207|go:"GO:0030674"(protein binding, bridging)|go:"GO:0035064"(methylated histone binding)|go:"GO:0070491"(repressing transcription factor binding)
## Interaction_Xrefs
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 658365: go:"GO:0000775"(chromosome, centromeric region)|go:"GO:0071962"(mitotic sister chromatid cohesion, centromeric)
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Annotations_interactor_A
## 1: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms|comment:"Stoichiometry: 1.0"
## 2: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 3: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 4: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## 5: comment:mint|no-uniprot-update:
## ---
## 658365: -
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Annotations_interactor_B
## 1: comment:"Stoichiometry: 1.0"
## 2: comment:mint|no-uniprot-update:
## 3: comment:mint|no-uniprot-update:
## 4: comment:mint|no-uniprot-update:
## 5: function:May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton|comment:mint|comment:homomint|function:Antibodies against AMPH are detected in patients with stiff-man syndrome, a rare disease of the central nervous system characterized by progressive rigidity of the body musculature with superimposed painful spasms
## ---
## 658365: -
## 658366: -
## 658367: -
## 658368: -
## 658369: -
## Interaction_annotations
## 1: comment:homomint|comment:domino|comment:mint
## 2: figure legend:F1 F2|comment:domino|comment:mint
## 3: figure legend:F1 F2|comment:domino|comment:mint
## 4: figure legend:F1 F2|comment:domino|comment:mint
## 5: figure legend:F1 F2|comment:domino|comment:mint
## ---
## 658365: figure legend:1C and 2A|comment:Colocalisation was observed during both interphase and mitosis in WT and KE mutant,; however the W174A mutant localized normally to centromeres in interphase but failed to localize to centromeres in mitosis.|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658366: figure legend:4B|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658367: figure legend:Table S1|3d-resolution:1.93A|3d-r-factors:Rworking 18.9%, Rfree 23 %|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658368: figure legend:Supp 2A|agonist:"nocodazole:-a microtubule-destabilising agent increasing the proportion of mitotic cells."|full coverage:Only protein-protein interactions|curation depth:imex curation
## 658369: figure legend:Supp 2A|agonist:"nocodazole:-a microtubule-destabilising agent increasing the proportion of mitotic cells."|full coverage:Only protein-protein interactions|curation depth:imex curation
## Host_organisms Interaction_parameters Creation_date Update_date
## 1: -1 - 2001/01/10 2014/10/16
## 2: -1 - 2001/01/10 2014/10/16
## 3: -1 - 2001/01/10 2014/10/16
## 4: -1 - 2001/01/10 2014/10/16
## 5: -1 - 2001/01/10 2014/10/16
## ---
## 658365: 9606 - 2016/11/21 2016/11/21
## 658366: -1 kd:0.18x10^-6(molar) 2016/11/21 2016/12/08
## 658367: -1 - 2016/11/21 2016/11/28
## 658368: 9606 - 2016/11/21 2016/12/08
## 658369: 9606 - 2016/11/21 2016/12/08
## Checksums_interactor_A
## 1: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 2: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 3: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 4: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## 5: rogid:cilZXZ3YLDI1s7n8WNRyUE6EnJQ-2
## ---
## 658365: rogid:yNQ+OVYYyR0Ls2cp6/xzBld1hyE9606
## 658366: rogid:rTa6IoM9PWfd6qOccSMZy1o0bBU9606
## 658367: rogid:rTa6IoM9PWfd6qOccSMZy1o0bBU9606
## 658368: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## 658369: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## Checksums_interactor_B
## 1: rogid:RA73eMbCn6F7MD0ItxF/V7QbjqM9606
## 2: rogid:lPy6gBhpgvyGSYgOqeHbjcqBtMQ-2
## 3: rogid:GsDnsVmAo8ZZoKTZ4/uDb2x+h3c-2
## 4: rogid:M+f6GE3SQXrMBiIVttW1MKhz3M0-2
## 5: rogid:vrgVrVoYr45cUe4X6L/zBAE1RtU9606
## ---
## 658365: rogid:+9LOzr4lV46zzZnWJVcLGeiB1Z09606
## 658366: rogid:W2npW/vFRcuTkStKpknsAP69q6I9606
## 658367: rogid:W2npW/vFRcuTkStKpknsAP69q6I9606
## 658368: rogid:4pmZhSoAp5JmH19k2tT+w3z9Hgo9606
## 658369: rogid:yNQ+OVYYyR0Ls2cp6/xzBld1hyE9606
## Interaction_Checksums
## 1: intact-crc:F4234557A3B54840|rigid:n+UcEH4PPLkFnIyvBiXrLefK/xU
## 2: intact-crc:880913D9000BF26E|rigid:iRObbQsaUeX0PxuKeQwZ73s8iKU
## 3: intact-crc:B68245E1F0508124|rigid:SlinPP5vIczFOGZjelrO+IXJq1s
## 4: intact-crc:8F7F46DF027DF34E|rigid:uiWbDe6gaj1XcnJXNxuLLq2l/m4
## 5: intact-crc:2EF43A66D9B2D428|rigid:/ki1zA46M4Q+rHcjCcxNhhk+5Xw
## ---
## 658365: rigid:S2Pj+tiJDfK8lcndvJ4suDk6dzc
## 658366: rigid:KF/f7qCgJl3XR/i3dS9sUX4LVck
## 658367: rigid:KF/f7qCgJl3XR/i3dS9sUX4LVck
## 658368: rigid:nFnJxwm0rB490rXXUFOd8T5H8rs
## 658369: rigid:nFnJxwm0rB490rXXUFOd8T5H8rs
## Negative
## 1: false
## 2: false
## 3: false
## 4: false
## 5: false
## ---
## 658365: false
## 658366: false
## 658367: false
## 658368: false
## 658369: false
## Features_interactor_A
## 1: binding-associated region:626-695(MINT-376295)
## 2: binding-associated region:626-695(MINT-8094602)
## 3: binding-associated region:626-695(MINT-8094630)
## 4: binding-associated region:626-695(MINT-8094654)
## 5: -
## ---
## 658365: Mutation having no effect on an interaction:89-91|mutation decreasing interaction strength:174-174|green fluorescent protein tag:?-?
## 658366: sufficient binding region:448-456
## 658367: sufficient binding region:448-456
## 658368: -
## 658369: -
## Features_interactor_B
## 1: binding-associated region:1063-1070(MINT-376288)
## 2: -
## 3: -
## 4: -
## 5: binding-associated region:626-695(MINT-8094680)
## ---
## 658365: necessary binding region:125-248|mcherry fluorescent protein tag:?-?
## 658366: sufficient binding region:108..108-185..185(IPR008251)
## 658367: sufficient binding region:108..108-185..185(IPR008251)
## 658368: -
## 658369: -
## Stoichiometrys_interactor_A Stoichiometrys_interactor_B
## 1: - -
## 2: - -
## 3: - -
## 4: - -
## 5: - -
## ---
## 658365: - -
## 658366: - -
## 658367: 1 2
## 658368: - -
## 658369: - -
## Identification_method_participant_A
## 1: psi-mi:"MI:0078"(nucleotide sequence identification)
## 2: psi-mi:"MI:0078"(nucleotide sequence identification)
## 3: psi-mi:"MI:0078"(nucleotide sequence identification)
## 4: psi-mi:"MI:0078"(nucleotide sequence identification)
## 5: psi-mi:"MI:0083"(peptide synthesis)
## ---
## 658365: psi-mi:"MI:0867"(tag visualisation by fluorescence)
## 658366: psi-mi:"MI:0396"(predetermined participant)
## 658367: psi-mi:"MI:0396"(predetermined participant)
## 658368: psi-mi:"MI:0113"(western blot)
## 658369: psi-mi:"MI:0113"(western blot)
## Identification_method_participant_B
## 1: psi-mi:"MI:0078"(nucleotide sequence identification)
## 2: psi-mi:"MI:0083"(peptide synthesis)
## 3: psi-mi:"MI:0083"(peptide synthesis)
## 4: psi-mi:"MI:0083"(peptide synthesis)
## 5: psi-mi:"MI:0078"(nucleotide sequence identification)
## ---
## 658365: psi-mi:"MI:0867"(tag visualisation by fluorescence)
## 658366: psi-mi:"MI:0396"(predetermined participant)
## 658367: psi-mi:"MI:0396"(predetermined participant)
## 658368: psi-mi:"MI:0113"(western blot)
## 658369: psi-mi:"MI:0113"(western blot)
## interactor_IDs_databases_A interactor_IDs_databases_B
## 1: uniprotkb uniprotkb
## 2: uniprotkb intact
## 3: uniprotkb intact
## 4: uniprotkb intact
## 5: intact uniprotkb
## ---
## 658365: uniprotkb uniprotkb
## 658366: uniprotkb uniprotkb
## 658367: uniprotkb uniprotkb
## 658368: uniprotkb uniprotkb
## 658369: uniprotkb uniprotkb
## bait_prey_status_A bait_prey_status_B IDs_interactor_A_isoforms
## 1: prey bait P49418
## 2: prey bait P49418
## 3: prey bait P49418
## 4: prey bait P49418
## 5: bait prey EBI-7121765
## ---
## 658365: neutral component neutral component P45973
## 658366: neutral component neutral component Q5FBB7
## 658367: unspecified role unspecified role Q5FBB7
## 658368: bait prey Q9NQS7
## 658369: bait prey Q9NQS7
## IDs_interactor_B_isoforms
## 1: O43426
## 2: EBI-7121639
## 3: EBI-7121654
## 4: EBI-7121715
## 5: P49418
## ---
## 658365: Q9NQS7
## 658366: P83916
## 658367: P83916
## 658368: Q96GD4
## 658369: P45973## copy all.IntAct (data.table doesn't make an explicit copy while assigning DT = data.table())
all.IntAct.modif = copy(all.IntAct)
## Uniprot to geneID mapping
#downloading the content of the folder containing species specific ID mapping
{
{# generating filenames
library(RCurl)
uniprotAC2geneID_url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
filenames <- getURL(uniprotAC2geneID_url,dirlistonly = TRUE)
filenames = unlist(strsplit(filenames,"\n"))
filenames = filenames[grep("idmapping.dat.gz",filenames)]
uniprotAC2geneID_filename = paste0("./Data/uniprotAC2geneID","release_", format(Sys.Date(), "%m-%Y"),"_", filenames)
uniprotAC2geneID_filename.dat = substr(uniprotAC2geneID_filename, 1, nchar(uniprotAC2geneID_filename)-3)
}
# downloading and unzipping files
for(i in 1:length(uniprotAC2geneID_filename.dat)){
if(!file.exists(uniprotAC2geneID_filename.dat[i])) {
downloader::download(paste0(uniprotAC2geneID_url,filenames[i]), uniprotAC2geneID_filename[i])
R.utils::gunzip(uniprotAC2geneID_filename[i])
# make git ignore big files
gitignore = c(substr(uniprotAC2geneID_filename.dat[i], 2, nchar(uniprotAC2geneID_filename.dat[i])),
readLines(".gitignore"))
write(gitignore, ".gitignore")
}
}
# reading files for uniprotAC to geneID mapping
uniprotAC2geneID = data.table()
for(i in 1:length(uniprotAC2geneID_filename.dat)){
temp = fread(uniprotAC2geneID_filename.dat[i], header = F)
temp = temp[V2 == "GeneID", .(V1, V3)]
uniprotAC2geneID = rbind(uniprotAC2geneID,temp)
rm(list = "temp")
}
}## Loading required package: bitops##
Read 75.0% of 1720326 rows
Read 1720326 rows and 3 (of 3) columns from 0.044 GB file in 00:00:03
##
Read 75.2% of 1290213 rows
Read 1290213 rows and 3 (of 3) columns from 0.035 GB file in 00:00:03
##
Read 18.4% of 5062402 rows
Read 18.8% of 5062402 rows
Read 60.1% of 5062402 rows
Read 5062402 rows and 3 (of 3) columns from 0.122 GB file in 00:00:07
##
Read 26.5% of 2190726 rows
Read 2190726 rows and 3 (of 3) columns from 0.055 GB file in 00:00:03## map GeneIDs for IDs_interactor_A
{
colnames(uniprotAC2geneID)[2] = "IDs_interactor_A_GeneID"
all.IntAct.modif = merge(x=all.IntAct.modif, y=uniprotAC2geneID, by.x = "IDs_interactor_A", by.y = "V1", all.x=TRUE, all.y = F)
}
## map GeneIDs for IDs_interactor_B
{
colnames(uniprotAC2geneID)[2] = "IDs_interactor_B_GeneID"
all.IntAct.modif = merge(x=all.IntAct.modif, y=uniprotAC2geneID, by.x = "IDs_interactor_B", by.y = "V1", all.x=TRUE, all.y = F)
rm(list = "uniprotAC2geneID")
}## getting the publication ID for each gene
{
geneID2pubmed_url = "ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz"
geneID2pubmed_filename = paste0("./Data/geneID2pubmed_release_", format(Sys.Date(), "%m-%Y.gz"))
geneID2pubmed_filename_txt = substr(geneID2pubmed_filename, 1, nchar(geneID2pubmed_filename)-3)
if(!file.exists(geneID2pubmed_filename_txt)) {
downloader::download(geneID2pubmed_url, geneID2pubmed_filename)
R.utils::gunzip(geneID2pubmed_filename)
gitignore = c(substr(geneID2pubmed_filename, 2, nchar(geneID2pubmed_filename)-3), readLines(".gitignore"))
write(gitignore, ".gitignore")
}
}
## count the number of pubmed PMID per GeneIDs for IDs_interactor_A and B
{
geneID2pubmed = fread(geneID2pubmed_filename_txt, colClasses = c("character","character","character"))
geneID2pubmed = geneID2pubmed[,.(GeneID, PubMed_ID)]
geneID2pubmed[, interactor_A_total_PMID := length(PubMed_ID), by = GeneID]
geneID2pubmed = geneID2pubmed[,unique(data.table(GeneID,interactor_A_total_PMID))][,GeneID := as.character(GeneID)]
all.IntAct.modif = merge(all.IntAct.modif, geneID2pubmed, by.x = "IDs_interactor_A_GeneID", by.y = "GeneID", all.x=TRUE)
colnames(geneID2pubmed)[2] = "interactor_B_total_PMID"
all.IntAct.modif = merge(all.IntAct.modif, geneID2pubmed, by.x = "IDs_interactor_B_GeneID", by.y = "GeneID", all.x=TRUE)
colnames(all.IntAct.modif)
rm(list = "geneID2pubmed")
}##
Read 19.7% of 9474810 rows
Read 22.3% of 9474810 rows
Read 65.4% of 9474810 rows
Read 83.2% of 9474810 rows
Read 99.5% of 9474810 rows
Read 9474810 rows and 3 (of 3) columns from 0.202 GB file in 00:00:12# Count the number of interactions per publication
{
all.IntAct.modif[,unique_interactions := apply(data.table(IDs_interactor_A,IDs_interactor_B,stringsAsFactors = F), 1,
function(a) { z = sort(a)
paste0(z[1],"_",z[2]) })]
all.IntAct.modif[,unique_interactions_per_Publication := length(unique(unique_interactions)), by = Publication_Identifiers]
all.IntAct.modif[,interaction_ids_per_Publication := length(unique(Interaction_identifiers)), by = Publication_Identifiers]
all.IntAct.modif[Expansion_methods != "psi-mi:\"MI:1060\"(spoke expansion)",unique_interactions_per_Publication_nospoke := length(unique(unique_interactions)),
by = Publication_Identifiers]
all.IntAct.modif[Expansion_methods != "psi-mi:\"MI:1060\"(spoke expansion)", interaction_ids_per_Publication_nospoke := length(unique(Interaction_identifiers)), by = Publication_Identifiers]
}## IDs_interactor_B_GeneID IDs_interactor_A_GeneID IDs_interactor_B
## 1: NA NA -
## 2: NA NA -
## 3: NA NA -
## 4: NA NA -
## 5: NA NA -
## ---
## 692857: 99982 22627 Q6ZQ88
## 692858: 99982 22627 Q6ZQ88
## 692859: 99982 30841 Q6ZQ88
## 692860: 99982 71950 Q6ZQ88
## 692861: 99982 81879 Q6ZQ88
## IDs_interactor_A
## 1: A0A0H3K900
## 2: A5U0E5
## 3: A6MW92
## 4: A6TG64
## 5: A8DS38
## ---
## 692857: P62259
## 692858: P62259
## 692859: Q6P1G2
## 692860: Q80Z64
## 692861: Q3UNW5
## Alt._IDs_interactor_A
## 1: intact:EBI-2465150
## 2: intact:EBI-6409272
## 3: intact:EBI-1792769
## 4: intact:EBI-8066161|intact:MINT-8392347
## 5: intact:EBI-6995359|intact:MINT-8187004
## ---
## 692857: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692858: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692859: intact:EBI-1216214|uniprotkb:Q3V396|uniprotkb:Q6PFD0|uniprotkb:Q6ZPE8|uniprotkb:Q9CSF7|uniprotkb:Q9QZN6
## 692860: intact:EBI-2312517|uniprotkb:Q6SMR1|uniprotkb:Q7TN85
## 692861: intact:EBI-5691372|uniprotkb:Q99PF2|uniprotkb:Q14AW3
## Alt._IDs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692858: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692859: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692860: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692861: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## Aliases_interactor_A
## 1: psi-mi:a0a0h3k900_staae(display_long)|uniprotkb:phoR(gene name)|psi-mi:phoR(display_short)|uniprotkb:NWMN_1585(locus name)
## 2: psi-mi:a5u0e5_mycta(display_long)|uniprotkb:phoP(gene name)|psi-mi:phoP(display_short)|uniprotkb:MRA_0767(locus name)
## 3: psi-mi:a6mw92_maize(display_long)|uniprotkb:bif2(gene name)|psi-mi:bif2(display_short)
## 4: psi-mi:a6tg64_klep7(display_long)|uniprotkb:Serine/threonine-protein kinase SrkA(gene name synonym)|uniprotkb:srkA(gene name synonym)|uniprotkb:KPN_04169(orf name)|uniprotkb:yihE(gene name)|psi-mi:yihE(display_short)
## 5: psi-mi:a8ds38_tabdi(display_long)
## ---
## 692857: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692858: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692859: psi-mi:kdm2b_mouse(display_long)|uniprotkb:Kdm2b(gene name)|psi-mi:Kdm2b(display_short)|uniprotkb:Fbl10(gene name synonym)|uniprotkb:Jhdm1b(gene name synonym)|uniprotkb:Kiaa3014(gene name synonym)|uniprotkb:[Histone-H3]-lysine-36 demethylase 1B(gene name synonym)|uniprotkb:F-box and leucine-rich repeat protein 10(gene name synonym)|uniprotkb:F-box/LRR-repeat protein 10(gene name synonym)|uniprotkb:F-box protein FBL10(gene name synonym)|uniprotkb:Fbxl10(gene name synonym)|uniprotkb:JmjC domain-containing histone demethylation protein 1B(gene name synonym)
## 692860: psi-mi:nanog_mouse(display_long)|uniprotkb:Nanog(gene name)|psi-mi:Nanog(display_short)|uniprotkb:Ecat4(gene name synonym)|uniprotkb:Enk(gene name synonym)|uniprotkb:Homeobox transcription factor Nanog(gene name synonym)|uniprotkb:Early embryo specific expression NK-type homeobox protein(gene name synonym)|uniprotkb:ES cell-associated protein 4(gene name synonym)
## 692861: psi-mi:tf2l1_mouse(display_long)|uniprotkb:Tfcp2l1(gene name)|psi-mi:Tfcp2l1(display_short)|uniprotkb:CP2-related transcriptional repressor 1(gene name synonym)|uniprotkb:Crtr1(gene name synonym)|uniprotkb:Tcfcp2l1(gene name synonym)
## Aliases_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692858: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692859: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692860: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692861: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## Interaction_detection_methods
## 1: psi-mi:"MI:0424"(protein kinase assay)
## 2: psi-mi:"MI:0030"(cross-linking study)
## 3: psi-mi:"MI:0424"(protein kinase assay)
## 4: psi-mi:"MI:0424"(protein kinase assay)
## 5: psi-mi:"MI:0435"(protease assay)
## ---
## 692857: psi-mi:"MI:0027"(cosedimentation)
## 692858: psi-mi:"MI:0027"(cosedimentation)
## 692859: psi-mi:"MI:0096"(pull down)
## 692860: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## 692861: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## Publication_1st_authors Publication_Identifiers
## 1: Casino et al. (2009) 19800110
## 2: Gupta et al. (2009) 19820095
## 3: Skirpan et al. (2008) 18466309
## 4: Srinivasan et al. (2012) 23010593
## 5: Dutta et al. (2011) 21707922
## ---
## 692857: Kislinger et al. (2006) 16615898
## 692858: Kislinger et al. (2006) 16615898
## 692859: Sanchez et al. (2007) 17296600
## 692860: Gagliardi et al. (2013) 23892456
## 692861: van et al. (2010) 20362541
## Taxid_interactor_A Taxid_interactor_B
## 1: 426430 -
## 2: 419947 -
## 3: 4577 -
## 4: 272620 -
## 5: 52861 -
## ---
## 692857: 10090 10090
## 692858: 10090 10090
## 692859: 10090 10090
## 692860: 10090 10090
## 692861: 10090 10090
## Interaction_types
## 1: psi-mi:"MI:0217"(phosphorylation reaction)
## 2: psi-mi:"MI:0915"(physical association)
## 3: psi-mi:"MI:0217"(phosphorylation reaction)
## 4: psi-mi:"MI:0217"(phosphorylation reaction)
## 5: psi-mi:"MI:0194"(cleavage reaction)
## ---
## 692857: psi-mi:"MI:0403"(colocalization)
## 692858: psi-mi:"MI:0403"(colocalization)
## 692859: psi-mi:"MI:0914"(association)
## 692860: psi-mi:"MI:0914"(association)
## 692861: psi-mi:"MI:0914"(association)
## Source_databases Interaction_identifiers Confidence_values
## 1: psi-mi:"MI:0469"(IntAct) EBI-2465076 0.44
## 2: psi-mi:"MI:0903"(mpidb) EBI-6409277 0.40
## 3: psi-mi:"MI:0469"(IntAct) EBI-1792855 NA
## 4: psi-mi:"MI:0471"(MINT) EBI-8066173 NA
## 5: psi-mi:"MI:0471"(MINT) EBI-6995391 NA
## ---
## 692857: psi-mi:"MI:0471"(MINT) EBI-8412660 0.35
## 692858: psi-mi:"MI:0471"(MINT) EBI-8459929 0.35
## 692859: psi-mi:"MI:0469"(IntAct) EBI-1249446 0.35
## 692860: psi-mi:"MI:0471"(MINT) EBI-8820601 0.35
## 692861: psi-mi:"MI:0469"(IntAct) EBI-5735888 0.35
## Expansion_methods
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:1060"(spoke expansion)
## 692858: psi-mi:"MI:1060"(spoke expansion)
## 692859: psi-mi:"MI:1060"(spoke expansion)
## 692860: psi-mi:"MI:1060"(spoke expansion)
## 692861: psi-mi:"MI:1060"(spoke expansion)
## Biological_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Biological_roles_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Experimental_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0497"(neutral component)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0497"(neutral component)
## 692858: psi-mi:"MI:0497"(neutral component)
## 692859: psi-mi:"MI:0496"(bait)
## 692860: psi-mi:"MI:0496"(bait)
## 692861: psi-mi:"MI:0496"(bait)
## Experimental_roles_interactor_B Types_interactor_A
## 1: - psi-mi:"MI:0326"(protein)
## 2: - psi-mi:"MI:0326"(protein)
## 3: - psi-mi:"MI:0326"(protein)
## 4: - psi-mi:"MI:0326"(protein)
## 5: - psi-mi:"MI:0326"(protein)
## ---
## 692857: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## Types_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0326"(protein)
## Xrefs_interactor_A
## 1: go:"GO:0005524"(ATP binding)|refseq:WP_000975269.1|uniprotkb:A6QHM5(uniprot-removed-ac)|go:"GO:0000155"(phosphorelay sensor kinase activity)|go:"GO:0005622"(intracellular)|go:"GO:0016021"(integral component of membrane)|interpro:IPR000014(PAS)|interpro:IPR003594(ATP-binding region, ATPase-like)|interpro:IPR003660(Signal transduction histidine kinase, HAMP region)|interpro:IPR003661(Signal transduction histidine kinase, subgroup 1, dimerisation and phosphoacceptor region)|interpro:IPR004358(Signal transduction histidine kinase-related protein, C-terminal)|interpro:IPR005467(Signal transduction histidine kinase, core)
## 2: refseq:WP_012054162.1|go:"GO:0005622"(intracellular)|go:"GO:0006351"(transcription, DNA-templated)|interpro:IPR016032(Signal transduction response regulator, C-terminal effector)|go:"GO:0003677"(DNA binding)|go:"GO:0006355"(regulation of transcription, DNA-templated)|interpro:IPR001789(Signal transduction response regulator, receiver region)|interpro:IPR001867(Signal transduction response regulator, C-terminal)|interpro:IPR011006(CheY-like)|interpro:IPR011991(Winged helix repressor DNA-binding)|go:"GO:0000160"(phosphorelay signal transduction system)
## 3: go:"GO:0004672"(protein kinase activity)|interpro:IPR011009(Protein kinase-like)|interpro:IPR000719(Protein kinase, core)|interpro:IPR008271(Serine/threonine protein kinase, active site)|go:"GO:0005524"(ATP binding)|refseq:NP_001106051.1
## 4: interpro:IPR032882|interpro:IPR011009(Protein kinase-like)|interpro:IPR002575(Aminoglycoside phosphotransferase)|refseq:WP_004187940.1|go:"GO:0000287"(magnesium ion binding)|go:"GO:0004674"(protein serine/threonine kinase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005737"(cytoplasm)|go:"GO:0006950"(response to stress)|mint:MINT-8392362(identity)
## 5: interpro:IPR025661|interpro:IPR000169(Peptidase, cysteine peptidase active site)|interpro:IPR013201(Proteinase inhibitor I29, cathepsin propeptide)|interpro:IPR013128(Peptidase C1A, papain)|interpro:IPR000668(Peptidase C1A, papain C-terminal)|go:"GO:0008234"(cysteine-type peptidase activity)|rcsb pdb:2PRE|mint:MINT-8187033(identity)
## ---
## 692857: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428681(identity)
## 692858: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428693(identity)
## 692859: interpro:IPR032675|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0030307"(positive regulation of cell growth)|go:"GO:0070544"(histone H3-K36 demethylation)|go:"GO:1902459"(positive regulation of stem cell population maintenance)|reactome:R-MMU-3214842|go:"GO:0030900"(forebrain development)|go:"GO:0030902"(hindbrain development)|go:"GO:0031519"(PcG protein complex)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0035518"(histone H2A monoubiquitination)|go:"GO:0005730"(nucleolus)|ensembl:ENSMUST00000031435|ensembl:ENSMUST00000046073|ensembl:ENSMUSG00000029475|ensembl:ENSMUSP00000031435|ensembl:ENSMUSP00000038229|interpro:IPR006553(Leucine-rich repeat, cysteine-containing subtype)|refseq:NP_038938.1|interpro:IPR001810(Cyclin-like F-box)|interpro:IPR003347(Transcription factor jumonji/aspartyl beta-hydroxylase)|interpro:IPR002857(Zinc finger, CXXC-type)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR019787|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|go:"GO:0051864"("histone demethylase activity (H3-K36 specific)")|go:"GO:0019843"(rRNA binding)|go:"GO:0008270"(zinc ion binding)|go:"GO:0048596"(embryonic camera-type eye morphogenesis)|go:"GO:0021592"(fourth ventricle development)|go:"GO:0021993"(initiation of neural tube closure)|go:"GO:0021670"(lateral ventricle development)|go:"GO:0030901"(midbrain development)|go:"GO:0021555"(midbrain-hindbrain boundary morphogenesis)|go:"GO:2000178"(negative regulation of neural precursor cell proliferation)|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0007283"(spermatogenesis)|go:"GO:0021678"(third ventricle development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_001003953.1
## 692860: go:"GO:2000036"(regulation of stem cell population maintenance)|go:"GO:0009825"(multidimensional cell growth)|go:"GO:0036018"(cellular response to erythropoietin)|go:"GO:0042246"(tissue regeneration)|go:"GO:0072752"(cellular response to rapamycin)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0001714"(endodermal cell fate specification)|go:"GO:0005730"(nucleolus)|go:"GO:0008283"(cell proliferation)|go:"GO:0035019"(somatic stem cell population maintenance)|go:"GO:0003677"(DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0010033"(response to organic substance)|go:"GO:0010454"(negative regulation of cell fate commitment)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0045596"(negative regulation of cell differentiation)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0048863"(stem cell differentiation)|ensembl:ENSMUSP00000012540|ensembl:ENSMUSP00000108199|ensembl:ENSMUSP00000108200|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0010468"(regulation of gene expression)|go:"GO:0045595"(regulation of cell differentiation)|ensembl:ENSMUST00000012540|ensembl:ENSMUST00000112580|ensembl:ENSMUST00000112581|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0003682"(chromatin binding)|go:"GO:0001158"(enhancer sequence-specific DNA binding)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0009880"(embryonic pattern specification)|go:"GO:0008406"(gonad development)|go:"GO:0001710"(mesodermal cell fate commitment)|go:"GO:0030514"(negative regulation of BMP signaling pathway)|go:"GO:0042664"(negative regulation of endodermal cell fate specification)|go:"GO:0008284"(positive regulation of cell proliferation)|go:"GO:0045931"(positive regulation of mitotic cell cycle)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0032526"(response to retinoic acid)|go:"GO:0017145"(stem cell division)|go:"GO:0019827"(stem cell population maintenance)|refseq:XP_006506714.1|refseq:NP_082292.1|ensembl:ENSMUSG00000012396|interpro:IPR001356(Homeobox)|interpro:IPR017970|interpro:IPR009057(Homeodomain-like)|rcsb pdb:2VI6|refseq:NP_001276757.1|refseq:NP_001276759.1|refseq:NP_001276760.1|go:"GO:0006351"(transcription, DNA-templated)
## 692861: go:"GO:0016020"(membrane)|go:"GO:0000902"(cell morphogenesis)|go:"GO:0007028"(cytoplasm organization)|go:"GO:0008340"(determination of adult lifespan)|go:"GO:0002070"(epithelial cell maturation)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0045927"(positive regulation of growth)|go:"GO:0007431"(salivary gland development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_076244.2|interpro:IPR007604(CP2 transcription factor)|interpro:IPR013761(Sterile alpha motif-type)|go:"GO:0005667"(transcription factor complex)|go:"GO:0005737"(cytoplasm)|go:"GO:0005634"(nucleus)|ensembl:ENSMUST00000027629|ensembl:ENSMUSG00000026380|ensembl:ENSMUSP00000027629|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0043565"(sequence-specific DNA binding)
## Xrefs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450494(identity)
## 692858: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450497(identity)
## 692859: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692860: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692861: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## Interaction_Xrefs
## 1: go:"GO:0046777"(protein autophosphorylation)|go:"GO:0004672"(protein kinase activity)
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0005634"(nucleus)
## 692858: go:"GO:0005634"(nucleus)
## 692859: go:"GO:0005634"(nucleus)
## 692860: go:"GO:0005634"(nucleus)
## 692861: -
## Annotations_interactor_A Annotations_interactor_B
## 1: - -
## 2: - -
## 3: - -
## 4: comment:mint -
## 5: comment:mint -
## ---
## 692857: spectral count:7 spectral count:5
## 692858: spectral count:9 spectral count:9
## 692859: - -
## 692860: - -
## 692861: - -
## Interaction_annotations
## 1: figure legend:Fig. 5F|full coverage:Only protein-protein interactions|curation depth:imex curation
## 2: figure legend:Fig. 5|full coverage:Only protein-protein interactions|curation depth:imex curation
## 3: figure legend:Figure 3|comment:Bif2 was shown to autophosphorylate.
## 4: figure legend:f1|comment:mint|intra-molecular:true
## 5: figure legend:sf1|comment:mint|intra-molecular:true
## ---
## 692857: figure legend:ST1|comment:mint
## 692858: figure legend:ST1|comment:mint
## 692859: figure legend:4A|dataset:Apoptosis - Interactions involving proteins with a function related to apoptosis|dataset:Chromatin - Epigenetic interactions resulting in chromatin modulation
## 692860: figure legend:t1 st1|full coverage:Only protein-protein interactions|curation depth:imex curation
## 692861: figure legend:Supplementary Table 4 + 8, Figure 2D.|full coverage:Only protein-protein interactions|curation depth:imex curation
## Host_organisms Interaction_parameters Creation_date Update_date
## 1: -1 - 2009/10/21 2014/10/16
## 2: -1 - 2012/11/30 2014/10/16
## 3: -1 - 2008/07/16 2014/10/16
## 4: -1 - 2012/09/10 2014/10/16
## 5: -1 - 2011/06/14 2014/10/16
## ---
## 692857: 10090 - 2007/03/13 2016/11/30
## 692858: 10090 - 2007/03/13 2016/11/30
## 692859: 10090 - 2007/03/21 2014/10/16
## 692860: 10090 - 2013/10/23 2014/10/16
## 692861: 10090 - 2012/02/29 2014/10/16
## Checksums_interactor_A
## 1: rogid:f1Y/+UDZ3WsP2yvsjJf94FntkZw426430
## 2: rogid:1SwukqEqW/H9T6naynkr9SAdtj4419947
## 3: rogid:oMrfj4TfaFdtkKv98ZNc7fCadrI4577
## 4: rogid:WfbB1DvDuvtchMuIkV17/YdCVlQ272620
## 5: rogid:6LtDcYFGc5XYs1zKx1uXRn4gZJs52861
## ---
## 692857: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692858: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692859: rogid:bNAPO2wQNjeaKjHXp02ErpRfSDw10090
## 692860: rogid:v8TDhd7PZnOKFS3djxouMHxftPs10090
## 692861: rogid:QtzNiWQU27XK2s0idF91/IAVi0E10090
## Checksums_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692858: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692859: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692860: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692861: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## Interaction_Checksums
## 1: intact-crc:7BBA0D1EA237FEC3
## 2: intact-crc:4096C84569EA780A
## 3: intact-crc:388A04F50F31D812
## 4: intact-crc:0313C9ADE7ADCCCC
## 5: intact-crc:40C3AD7BE9F4C193
## ---
## 692857: intact-crc:A16CFA73CF6AE082
## 692858: intact-crc:1B66D582CA1FAD01
## 692859: intact-crc:75642DE2B905DD44|rigid:W0bsCwxpYX8+OuDZDxj7QMajzgM
## 692860: intact-crc:B3ED58BF30D17C05|rigid:b8XXlh+d4ezd3xoFuCzS1wEcnOs
## 692861: intact-crc:8889A2183786C4BC|rigid:qPM+mcj1rQf5up/kjdxdiC3xoHo
## Negative
## 1: false
## 2: false
## 3: false
## 4: false
## 5: false
## ---
## 692857: false
## 692858: false
## 692859: false
## 692860: false
## 692861: false
## Features_interactor_A
## 1: sufficient binding region:316-554(IPR005467)
## 2: his tag:n-n|mutation increasing interaction strength:21-21
## 3: glutathione s tranferase tag:?-?|mutation disrupting interaction:161-161|mutation disrupting interaction:258-258
## 4: -
## 5: his tag:?-?(MINT-8187036)
## ---
## 692857: -
## 692858: -
## 692859: fusion protein:n-n|biotin tag:n-n
## 692860: flag tag:?-?
## 692861: flag tag:c-c
## Features_interactor_B Stoichiometrys_interactor_A
## 1: - -
## 2: - 1
## 3: - -
## 4: - -
## 5: - -
## ---
## 692857: - -
## 692858: - -
## 692859: - -
## 692860: - -
## 692861: - -
## Stoichiometrys_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: -
## 692858: -
## 692859: -
## 692860: -
## 692861: -
## Identification_method_participant_A
## 1: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 2: psi-mi:"MI:0396"(predetermined participant)
## 3: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 4: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 5: psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## Identification_method_participant_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## interactor_IDs_databases_A interactor_IDs_databases_B
## 1: uniprotkb -
## 2: uniprotkb -
## 3: uniprotkb -
## 4: uniprotkb -
## 5: uniprotkb -
## ---
## 692857: uniprotkb uniprotkb
## 692858: uniprotkb uniprotkb
## 692859: uniprotkb uniprotkb
## 692860: uniprotkb uniprotkb
## 692861: uniprotkb uniprotkb
## bait_prey_status_A bait_prey_status_B IDs_interactor_A_isoforms
## 1: self - A0A0H3K900
## 2: neutral component - A5U0E5
## 3: putative self - A6MW92
## 4: self - A6TG64
## 5: self - A8DS38
## ---
## 692857: neutral component neutral component P62259
## 692858: neutral component neutral component P62259
## 692859: bait prey Q6P1G2
## 692860: bait prey Q80Z64
## 692861: bait prey Q3UNW5
## IDs_interactor_B_isoforms interactor_A_total_PMID
## 1: - NA
## 2: - NA
## 3: - NA
## 4: - NA
## 5: - NA
## ---
## 692857: Q6ZQ88 95
## 692858: Q6ZQ88 95
## 692859: Q6ZQ88 49
## 692860: Q6ZQ88 332
## 692861: Q6ZQ88 39
## interactor_B_total_PMID unique_interactions
## 1: NA -_A0A0H3K900
## 2: NA -_A5U0E5
## 3: NA -_A6MW92
## 4: NA -_A6TG64
## 5: NA -_A8DS38
## ---
## 692857: 103 P62259_Q6ZQ88
## 692858: 103 P62259_Q6ZQ88
## 692859: 103 Q6P1G2_Q6ZQ88
## 692860: 103 Q6ZQ88_Q80Z64
## 692861: 103 Q3UNW5_Q6ZQ88
## unique_interactions_per_Publication
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: 6557
## 692858: 6557
## 692859: 61
## 692860: 137
## 692861: 282
## interaction_ids_per_Publication
## 1: 9
## 2: 3
## 3: 6
## 4: 1
## 5: 2
## ---
## 692857: 24
## 692858: 24
## 692859: 10
## 692860: 12
## 692861: 60
## unique_interactions_per_Publication_nospoke
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: NA
## 692858: NA
## 692859: NA
## 692860: NA
## 692861: NA
## interaction_ids_per_Publication_nospoke
## 1: 9
## 2: 3
## 3: 6
## 4: 1
## 5: 2
## ---
## 692857: NA
## 692858: NA
## 692859: NA
## 692860: NA
## 692861: NA{
# selecting large scale / small scale threshold
library(rafalib)
mypar(1,2)
plot(log10(all.IntAct.modif$interaction_ids_per_Publication),
log10(all.IntAct.modif$unique_interactions_per_Publication),
main = "EBI interaction IDs per Publication vs unique interactions per Publication",
ylab = "unique interactions per Publication \n spoke-expanded interactions included",
xlab = "EBI interaction IDs per Publication")
plot(log10(all.IntAct.modif[Expansion_methods != "psi-mi:\"MI:1060\"(spoke expansion)",
unique_interactions_per_Publication_nospoke]),
log10(all.IntAct.modif[Expansion_methods != "psi-mi:\"MI:1060\"(spoke expansion)",
interaction_ids_per_Publication_nospoke]),
main = "unique interactions per Publication \n vs EBI interaction IDs per Publication",
xlab = "unique interactions per Publication \n spoke-expanded interactions excluded",
ylab = "EBI interaction IDs per Publication")
mypar(1,2)
hist(log10(all.IntAct.modif[,unique(data.table(unique_interactions_per_Publication,Publication_Identifiers))][,unique_interactions_per_Publication]),30, ylim = c(0,100))
abline(v = 2)
hist(log10(all.IntAct.modif[,unique(data.table(interaction_ids_per_Publication,Publication_Identifiers))][,interaction_ids_per_Publication]),30, ylim = c(0,100))
abline(v = 2)
}
# tag interactions by the scale of the study
{
# tagging interactons
all.IntAct.modif[,large_scale := as.numeric(interaction_ids_per_Publication > 100)]
all.IntAct.modif[,small_scale := as.numeric(interaction_ids_per_Publication <= 100)]
}## IDs_interactor_B_GeneID IDs_interactor_A_GeneID IDs_interactor_B
## 1: NA NA -
## 2: NA NA -
## 3: NA NA -
## 4: NA NA -
## 5: NA NA -
## ---
## 692857: 99982 22627 Q6ZQ88
## 692858: 99982 22627 Q6ZQ88
## 692859: 99982 30841 Q6ZQ88
## 692860: 99982 71950 Q6ZQ88
## 692861: 99982 81879 Q6ZQ88
## IDs_interactor_A
## 1: A0A0H3K900
## 2: A5U0E5
## 3: A6MW92
## 4: A6TG64
## 5: A8DS38
## ---
## 692857: P62259
## 692858: P62259
## 692859: Q6P1G2
## 692860: Q80Z64
## 692861: Q3UNW5
## Alt._IDs_interactor_A
## 1: intact:EBI-2465150
## 2: intact:EBI-6409272
## 3: intact:EBI-1792769
## 4: intact:EBI-8066161|intact:MINT-8392347
## 5: intact:EBI-6995359|intact:MINT-8187004
## ---
## 692857: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692858: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692859: intact:EBI-1216214|uniprotkb:Q3V396|uniprotkb:Q6PFD0|uniprotkb:Q6ZPE8|uniprotkb:Q9CSF7|uniprotkb:Q9QZN6
## 692860: intact:EBI-2312517|uniprotkb:Q6SMR1|uniprotkb:Q7TN85
## 692861: intact:EBI-5691372|uniprotkb:Q99PF2|uniprotkb:Q14AW3
## Alt._IDs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692858: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692859: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692860: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692861: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## Aliases_interactor_A
## 1: psi-mi:a0a0h3k900_staae(display_long)|uniprotkb:phoR(gene name)|psi-mi:phoR(display_short)|uniprotkb:NWMN_1585(locus name)
## 2: psi-mi:a5u0e5_mycta(display_long)|uniprotkb:phoP(gene name)|psi-mi:phoP(display_short)|uniprotkb:MRA_0767(locus name)
## 3: psi-mi:a6mw92_maize(display_long)|uniprotkb:bif2(gene name)|psi-mi:bif2(display_short)
## 4: psi-mi:a6tg64_klep7(display_long)|uniprotkb:Serine/threonine-protein kinase SrkA(gene name synonym)|uniprotkb:srkA(gene name synonym)|uniprotkb:KPN_04169(orf name)|uniprotkb:yihE(gene name)|psi-mi:yihE(display_short)
## 5: psi-mi:a8ds38_tabdi(display_long)
## ---
## 692857: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692858: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692859: psi-mi:kdm2b_mouse(display_long)|uniprotkb:Kdm2b(gene name)|psi-mi:Kdm2b(display_short)|uniprotkb:Fbl10(gene name synonym)|uniprotkb:Jhdm1b(gene name synonym)|uniprotkb:Kiaa3014(gene name synonym)|uniprotkb:[Histone-H3]-lysine-36 demethylase 1B(gene name synonym)|uniprotkb:F-box and leucine-rich repeat protein 10(gene name synonym)|uniprotkb:F-box/LRR-repeat protein 10(gene name synonym)|uniprotkb:F-box protein FBL10(gene name synonym)|uniprotkb:Fbxl10(gene name synonym)|uniprotkb:JmjC domain-containing histone demethylation protein 1B(gene name synonym)
## 692860: psi-mi:nanog_mouse(display_long)|uniprotkb:Nanog(gene name)|psi-mi:Nanog(display_short)|uniprotkb:Ecat4(gene name synonym)|uniprotkb:Enk(gene name synonym)|uniprotkb:Homeobox transcription factor Nanog(gene name synonym)|uniprotkb:Early embryo specific expression NK-type homeobox protein(gene name synonym)|uniprotkb:ES cell-associated protein 4(gene name synonym)
## 692861: psi-mi:tf2l1_mouse(display_long)|uniprotkb:Tfcp2l1(gene name)|psi-mi:Tfcp2l1(display_short)|uniprotkb:CP2-related transcriptional repressor 1(gene name synonym)|uniprotkb:Crtr1(gene name synonym)|uniprotkb:Tcfcp2l1(gene name synonym)
## Aliases_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692858: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692859: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692860: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692861: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## Interaction_detection_methods
## 1: psi-mi:"MI:0424"(protein kinase assay)
## 2: psi-mi:"MI:0030"(cross-linking study)
## 3: psi-mi:"MI:0424"(protein kinase assay)
## 4: psi-mi:"MI:0424"(protein kinase assay)
## 5: psi-mi:"MI:0435"(protease assay)
## ---
## 692857: psi-mi:"MI:0027"(cosedimentation)
## 692858: psi-mi:"MI:0027"(cosedimentation)
## 692859: psi-mi:"MI:0096"(pull down)
## 692860: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## 692861: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## Publication_1st_authors Publication_Identifiers
## 1: Casino et al. (2009) 19800110
## 2: Gupta et al. (2009) 19820095
## 3: Skirpan et al. (2008) 18466309
## 4: Srinivasan et al. (2012) 23010593
## 5: Dutta et al. (2011) 21707922
## ---
## 692857: Kislinger et al. (2006) 16615898
## 692858: Kislinger et al. (2006) 16615898
## 692859: Sanchez et al. (2007) 17296600
## 692860: Gagliardi et al. (2013) 23892456
## 692861: van et al. (2010) 20362541
## Taxid_interactor_A Taxid_interactor_B
## 1: 426430 -
## 2: 419947 -
## 3: 4577 -
## 4: 272620 -
## 5: 52861 -
## ---
## 692857: 10090 10090
## 692858: 10090 10090
## 692859: 10090 10090
## 692860: 10090 10090
## 692861: 10090 10090
## Interaction_types
## 1: psi-mi:"MI:0217"(phosphorylation reaction)
## 2: psi-mi:"MI:0915"(physical association)
## 3: psi-mi:"MI:0217"(phosphorylation reaction)
## 4: psi-mi:"MI:0217"(phosphorylation reaction)
## 5: psi-mi:"MI:0194"(cleavage reaction)
## ---
## 692857: psi-mi:"MI:0403"(colocalization)
## 692858: psi-mi:"MI:0403"(colocalization)
## 692859: psi-mi:"MI:0914"(association)
## 692860: psi-mi:"MI:0914"(association)
## 692861: psi-mi:"MI:0914"(association)
## Source_databases Interaction_identifiers Confidence_values
## 1: psi-mi:"MI:0469"(IntAct) EBI-2465076 0.44
## 2: psi-mi:"MI:0903"(mpidb) EBI-6409277 0.40
## 3: psi-mi:"MI:0469"(IntAct) EBI-1792855 NA
## 4: psi-mi:"MI:0471"(MINT) EBI-8066173 NA
## 5: psi-mi:"MI:0471"(MINT) EBI-6995391 NA
## ---
## 692857: psi-mi:"MI:0471"(MINT) EBI-8412660 0.35
## 692858: psi-mi:"MI:0471"(MINT) EBI-8459929 0.35
## 692859: psi-mi:"MI:0469"(IntAct) EBI-1249446 0.35
## 692860: psi-mi:"MI:0471"(MINT) EBI-8820601 0.35
## 692861: psi-mi:"MI:0469"(IntAct) EBI-5735888 0.35
## Expansion_methods
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:1060"(spoke expansion)
## 692858: psi-mi:"MI:1060"(spoke expansion)
## 692859: psi-mi:"MI:1060"(spoke expansion)
## 692860: psi-mi:"MI:1060"(spoke expansion)
## 692861: psi-mi:"MI:1060"(spoke expansion)
## Biological_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Biological_roles_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Experimental_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0497"(neutral component)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0497"(neutral component)
## 692858: psi-mi:"MI:0497"(neutral component)
## 692859: psi-mi:"MI:0496"(bait)
## 692860: psi-mi:"MI:0496"(bait)
## 692861: psi-mi:"MI:0496"(bait)
## Experimental_roles_interactor_B Types_interactor_A
## 1: - psi-mi:"MI:0326"(protein)
## 2: - psi-mi:"MI:0326"(protein)
## 3: - psi-mi:"MI:0326"(protein)
## 4: - psi-mi:"MI:0326"(protein)
## 5: - psi-mi:"MI:0326"(protein)
## ---
## 692857: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## Types_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0326"(protein)
## Xrefs_interactor_A
## 1: go:"GO:0005524"(ATP binding)|refseq:WP_000975269.1|uniprotkb:A6QHM5(uniprot-removed-ac)|go:"GO:0000155"(phosphorelay sensor kinase activity)|go:"GO:0005622"(intracellular)|go:"GO:0016021"(integral component of membrane)|interpro:IPR000014(PAS)|interpro:IPR003594(ATP-binding region, ATPase-like)|interpro:IPR003660(Signal transduction histidine kinase, HAMP region)|interpro:IPR003661(Signal transduction histidine kinase, subgroup 1, dimerisation and phosphoacceptor region)|interpro:IPR004358(Signal transduction histidine kinase-related protein, C-terminal)|interpro:IPR005467(Signal transduction histidine kinase, core)
## 2: refseq:WP_012054162.1|go:"GO:0005622"(intracellular)|go:"GO:0006351"(transcription, DNA-templated)|interpro:IPR016032(Signal transduction response regulator, C-terminal effector)|go:"GO:0003677"(DNA binding)|go:"GO:0006355"(regulation of transcription, DNA-templated)|interpro:IPR001789(Signal transduction response regulator, receiver region)|interpro:IPR001867(Signal transduction response regulator, C-terminal)|interpro:IPR011006(CheY-like)|interpro:IPR011991(Winged helix repressor DNA-binding)|go:"GO:0000160"(phosphorelay signal transduction system)
## 3: go:"GO:0004672"(protein kinase activity)|interpro:IPR011009(Protein kinase-like)|interpro:IPR000719(Protein kinase, core)|interpro:IPR008271(Serine/threonine protein kinase, active site)|go:"GO:0005524"(ATP binding)|refseq:NP_001106051.1
## 4: interpro:IPR032882|interpro:IPR011009(Protein kinase-like)|interpro:IPR002575(Aminoglycoside phosphotransferase)|refseq:WP_004187940.1|go:"GO:0000287"(magnesium ion binding)|go:"GO:0004674"(protein serine/threonine kinase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005737"(cytoplasm)|go:"GO:0006950"(response to stress)|mint:MINT-8392362(identity)
## 5: interpro:IPR025661|interpro:IPR000169(Peptidase, cysteine peptidase active site)|interpro:IPR013201(Proteinase inhibitor I29, cathepsin propeptide)|interpro:IPR013128(Peptidase C1A, papain)|interpro:IPR000668(Peptidase C1A, papain C-terminal)|go:"GO:0008234"(cysteine-type peptidase activity)|rcsb pdb:2PRE|mint:MINT-8187033(identity)
## ---
## 692857: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428681(identity)
## 692858: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428693(identity)
## 692859: interpro:IPR032675|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0030307"(positive regulation of cell growth)|go:"GO:0070544"(histone H3-K36 demethylation)|go:"GO:1902459"(positive regulation of stem cell population maintenance)|reactome:R-MMU-3214842|go:"GO:0030900"(forebrain development)|go:"GO:0030902"(hindbrain development)|go:"GO:0031519"(PcG protein complex)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0035518"(histone H2A monoubiquitination)|go:"GO:0005730"(nucleolus)|ensembl:ENSMUST00000031435|ensembl:ENSMUST00000046073|ensembl:ENSMUSG00000029475|ensembl:ENSMUSP00000031435|ensembl:ENSMUSP00000038229|interpro:IPR006553(Leucine-rich repeat, cysteine-containing subtype)|refseq:NP_038938.1|interpro:IPR001810(Cyclin-like F-box)|interpro:IPR003347(Transcription factor jumonji/aspartyl beta-hydroxylase)|interpro:IPR002857(Zinc finger, CXXC-type)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR019787|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|go:"GO:0051864"("histone demethylase activity (H3-K36 specific)")|go:"GO:0019843"(rRNA binding)|go:"GO:0008270"(zinc ion binding)|go:"GO:0048596"(embryonic camera-type eye morphogenesis)|go:"GO:0021592"(fourth ventricle development)|go:"GO:0021993"(initiation of neural tube closure)|go:"GO:0021670"(lateral ventricle development)|go:"GO:0030901"(midbrain development)|go:"GO:0021555"(midbrain-hindbrain boundary morphogenesis)|go:"GO:2000178"(negative regulation of neural precursor cell proliferation)|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0007283"(spermatogenesis)|go:"GO:0021678"(third ventricle development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_001003953.1
## 692860: go:"GO:2000036"(regulation of stem cell population maintenance)|go:"GO:0009825"(multidimensional cell growth)|go:"GO:0036018"(cellular response to erythropoietin)|go:"GO:0042246"(tissue regeneration)|go:"GO:0072752"(cellular response to rapamycin)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0001714"(endodermal cell fate specification)|go:"GO:0005730"(nucleolus)|go:"GO:0008283"(cell proliferation)|go:"GO:0035019"(somatic stem cell population maintenance)|go:"GO:0003677"(DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0010033"(response to organic substance)|go:"GO:0010454"(negative regulation of cell fate commitment)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0045596"(negative regulation of cell differentiation)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0048863"(stem cell differentiation)|ensembl:ENSMUSP00000012540|ensembl:ENSMUSP00000108199|ensembl:ENSMUSP00000108200|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0010468"(regulation of gene expression)|go:"GO:0045595"(regulation of cell differentiation)|ensembl:ENSMUST00000012540|ensembl:ENSMUST00000112580|ensembl:ENSMUST00000112581|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0003682"(chromatin binding)|go:"GO:0001158"(enhancer sequence-specific DNA binding)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0009880"(embryonic pattern specification)|go:"GO:0008406"(gonad development)|go:"GO:0001710"(mesodermal cell fate commitment)|go:"GO:0030514"(negative regulation of BMP signaling pathway)|go:"GO:0042664"(negative regulation of endodermal cell fate specification)|go:"GO:0008284"(positive regulation of cell proliferation)|go:"GO:0045931"(positive regulation of mitotic cell cycle)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0032526"(response to retinoic acid)|go:"GO:0017145"(stem cell division)|go:"GO:0019827"(stem cell population maintenance)|refseq:XP_006506714.1|refseq:NP_082292.1|ensembl:ENSMUSG00000012396|interpro:IPR001356(Homeobox)|interpro:IPR017970|interpro:IPR009057(Homeodomain-like)|rcsb pdb:2VI6|refseq:NP_001276757.1|refseq:NP_001276759.1|refseq:NP_001276760.1|go:"GO:0006351"(transcription, DNA-templated)
## 692861: go:"GO:0016020"(membrane)|go:"GO:0000902"(cell morphogenesis)|go:"GO:0007028"(cytoplasm organization)|go:"GO:0008340"(determination of adult lifespan)|go:"GO:0002070"(epithelial cell maturation)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0045927"(positive regulation of growth)|go:"GO:0007431"(salivary gland development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_076244.2|interpro:IPR007604(CP2 transcription factor)|interpro:IPR013761(Sterile alpha motif-type)|go:"GO:0005667"(transcription factor complex)|go:"GO:0005737"(cytoplasm)|go:"GO:0005634"(nucleus)|ensembl:ENSMUST00000027629|ensembl:ENSMUSG00000026380|ensembl:ENSMUSP00000027629|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0043565"(sequence-specific DNA binding)
## Xrefs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450494(identity)
## 692858: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450497(identity)
## 692859: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692860: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692861: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## Interaction_Xrefs
## 1: go:"GO:0046777"(protein autophosphorylation)|go:"GO:0004672"(protein kinase activity)
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0005634"(nucleus)
## 692858: go:"GO:0005634"(nucleus)
## 692859: go:"GO:0005634"(nucleus)
## 692860: go:"GO:0005634"(nucleus)
## 692861: -
## Annotations_interactor_A Annotations_interactor_B
## 1: - -
## 2: - -
## 3: - -
## 4: comment:mint -
## 5: comment:mint -
## ---
## 692857: spectral count:7 spectral count:5
## 692858: spectral count:9 spectral count:9
## 692859: - -
## 692860: - -
## 692861: - -
## Interaction_annotations
## 1: figure legend:Fig. 5F|full coverage:Only protein-protein interactions|curation depth:imex curation
## 2: figure legend:Fig. 5|full coverage:Only protein-protein interactions|curation depth:imex curation
## 3: figure legend:Figure 3|comment:Bif2 was shown to autophosphorylate.
## 4: figure legend:f1|comment:mint|intra-molecular:true
## 5: figure legend:sf1|comment:mint|intra-molecular:true
## ---
## 692857: figure legend:ST1|comment:mint
## 692858: figure legend:ST1|comment:mint
## 692859: figure legend:4A|dataset:Apoptosis - Interactions involving proteins with a function related to apoptosis|dataset:Chromatin - Epigenetic interactions resulting in chromatin modulation
## 692860: figure legend:t1 st1|full coverage:Only protein-protein interactions|curation depth:imex curation
## 692861: figure legend:Supplementary Table 4 + 8, Figure 2D.|full coverage:Only protein-protein interactions|curation depth:imex curation
## Host_organisms Interaction_parameters Creation_date Update_date
## 1: -1 - 2009/10/21 2014/10/16
## 2: -1 - 2012/11/30 2014/10/16
## 3: -1 - 2008/07/16 2014/10/16
## 4: -1 - 2012/09/10 2014/10/16
## 5: -1 - 2011/06/14 2014/10/16
## ---
## 692857: 10090 - 2007/03/13 2016/11/30
## 692858: 10090 - 2007/03/13 2016/11/30
## 692859: 10090 - 2007/03/21 2014/10/16
## 692860: 10090 - 2013/10/23 2014/10/16
## 692861: 10090 - 2012/02/29 2014/10/16
## Checksums_interactor_A
## 1: rogid:f1Y/+UDZ3WsP2yvsjJf94FntkZw426430
## 2: rogid:1SwukqEqW/H9T6naynkr9SAdtj4419947
## 3: rogid:oMrfj4TfaFdtkKv98ZNc7fCadrI4577
## 4: rogid:WfbB1DvDuvtchMuIkV17/YdCVlQ272620
## 5: rogid:6LtDcYFGc5XYs1zKx1uXRn4gZJs52861
## ---
## 692857: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692858: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692859: rogid:bNAPO2wQNjeaKjHXp02ErpRfSDw10090
## 692860: rogid:v8TDhd7PZnOKFS3djxouMHxftPs10090
## 692861: rogid:QtzNiWQU27XK2s0idF91/IAVi0E10090
## Checksums_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692858: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692859: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692860: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692861: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## Interaction_Checksums
## 1: intact-crc:7BBA0D1EA237FEC3
## 2: intact-crc:4096C84569EA780A
## 3: intact-crc:388A04F50F31D812
## 4: intact-crc:0313C9ADE7ADCCCC
## 5: intact-crc:40C3AD7BE9F4C193
## ---
## 692857: intact-crc:A16CFA73CF6AE082
## 692858: intact-crc:1B66D582CA1FAD01
## 692859: intact-crc:75642DE2B905DD44|rigid:W0bsCwxpYX8+OuDZDxj7QMajzgM
## 692860: intact-crc:B3ED58BF30D17C05|rigid:b8XXlh+d4ezd3xoFuCzS1wEcnOs
## 692861: intact-crc:8889A2183786C4BC|rigid:qPM+mcj1rQf5up/kjdxdiC3xoHo
## Negative
## 1: false
## 2: false
## 3: false
## 4: false
## 5: false
## ---
## 692857: false
## 692858: false
## 692859: false
## 692860: false
## 692861: false
## Features_interactor_A
## 1: sufficient binding region:316-554(IPR005467)
## 2: his tag:n-n|mutation increasing interaction strength:21-21
## 3: glutathione s tranferase tag:?-?|mutation disrupting interaction:161-161|mutation disrupting interaction:258-258
## 4: -
## 5: his tag:?-?(MINT-8187036)
## ---
## 692857: -
## 692858: -
## 692859: fusion protein:n-n|biotin tag:n-n
## 692860: flag tag:?-?
## 692861: flag tag:c-c
## Features_interactor_B Stoichiometrys_interactor_A
## 1: - -
## 2: - 1
## 3: - -
## 4: - -
## 5: - -
## ---
## 692857: - -
## 692858: - -
## 692859: - -
## 692860: - -
## 692861: - -
## Stoichiometrys_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: -
## 692858: -
## 692859: -
## 692860: -
## 692861: -
## Identification_method_participant_A
## 1: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 2: psi-mi:"MI:0396"(predetermined participant)
## 3: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 4: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 5: psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## Identification_method_participant_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## interactor_IDs_databases_A interactor_IDs_databases_B
## 1: uniprotkb -
## 2: uniprotkb -
## 3: uniprotkb -
## 4: uniprotkb -
## 5: uniprotkb -
## ---
## 692857: uniprotkb uniprotkb
## 692858: uniprotkb uniprotkb
## 692859: uniprotkb uniprotkb
## 692860: uniprotkb uniprotkb
## 692861: uniprotkb uniprotkb
## bait_prey_status_A bait_prey_status_B IDs_interactor_A_isoforms
## 1: self - A0A0H3K900
## 2: neutral component - A5U0E5
## 3: putative self - A6MW92
## 4: self - A6TG64
## 5: self - A8DS38
## ---
## 692857: neutral component neutral component P62259
## 692858: neutral component neutral component P62259
## 692859: bait prey Q6P1G2
## 692860: bait prey Q80Z64
## 692861: bait prey Q3UNW5
## IDs_interactor_B_isoforms interactor_A_total_PMID
## 1: - NA
## 2: - NA
## 3: - NA
## 4: - NA
## 5: - NA
## ---
## 692857: Q6ZQ88 95
## 692858: Q6ZQ88 95
## 692859: Q6ZQ88 49
## 692860: Q6ZQ88 332
## 692861: Q6ZQ88 39
## interactor_B_total_PMID unique_interactions
## 1: NA -_A0A0H3K900
## 2: NA -_A5U0E5
## 3: NA -_A6MW92
## 4: NA -_A6TG64
## 5: NA -_A8DS38
## ---
## 692857: 103 P62259_Q6ZQ88
## 692858: 103 P62259_Q6ZQ88
## 692859: 103 Q6P1G2_Q6ZQ88
## 692860: 103 Q6ZQ88_Q80Z64
## 692861: 103 Q3UNW5_Q6ZQ88
## unique_interactions_per_Publication
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: 6557
## 692858: 6557
## 692859: 61
## 692860: 137
## 692861: 282
## interaction_ids_per_Publication
## 1: 9
## 2: 3
## 3: 6
## 4: 1
## 5: 2
## ---
## 692857: 24
## 692858: 24
## 692859: 10
## 692860: 12
## 692861: 60
## unique_interactions_per_Publication_nospoke
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: NA
## 692858: NA
## 692859: NA
## 692860: NA
## 692861: NA
## interaction_ids_per_Publication_nospoke large_scale small_scale
## 1: 9 0 1
## 2: 3 0 1
## 3: 6 0 1
## 4: 1 0 1
## 5: 2 0 1
## ---
## 692857: NA 0 1
## 692858: NA 0 1
## 692859: NA 0 1
## 692860: NA 0 1
## 692861: NA 0 1#Count the number of interactions formed by proteins encoded by GeneID
{
all.IntAct.modif[,unique_interactions_isoforms := apply(data.table(IDs_interactor_A_isoforms,IDs_interactor_B_isoforms,stringsAsFactors = F), 1,
function(a) { z = sort(a)
paste0(z[1],"_",z[2]) })]
#====================
#UniprotID
all.IntAct.modif[,unique_interactions_per_interactor_A := length(unique(grep(IDs_interactor_A, unique_interactions ,value = T))), by = IDs_interactor_A]
all.IntAct.modif[,unique_interactions_per_interactor_B := length(unique(grep(IDs_interactor_B, unique_interactions ,value = T))), by = IDs_interactor_B]
#GeneID
# all.IntAct.modif[,unique_interactions_per_interactor_A_GeneID := length(unique(grep(IDs_interactor_A, unique_interactions ,value = T))), by = IDs_interactor_A_GeneID]
# all.IntAct.modif[,unique_interactions_per_interactor_B_GeneID := length(unique(grep(IDs_interactor_B, unique_interactions ,value = T))), by = IDs_interactor_B_GeneID]
# all.IntAct.modif[is.na(IDs_interactor_A_GeneID),unique_interactions_per_interactor_A_GeneID := NA]
# all.IntAct.modif[is.na(IDs_interactor_B_GeneID),unique_interactions_per_interactor_B_GeneID := NA]
#UniprotID isoform
# all.IntAct.modif[,unique_interactions_per_interactor_A_isoforms := length(unique(grep(IDs_interactor_A_isoforms, unique_interactions_isoforms ,value = T))), by = IDs_interactor_A_isoforms]
# all.IntAct.modif[,unique_interactions_per_interactor_B_isoforms := length(unique(grep(IDs_interactor_B_isoforms, unique_interactions_isoforms ,value = T))), by = IDs_interactor_B_isoforms]
}## IDs_interactor_B_GeneID IDs_interactor_A_GeneID IDs_interactor_B
## 1: NA NA -
## 2: NA NA -
## 3: NA NA -
## 4: NA NA -
## 5: NA NA -
## ---
## 692857: 99982 22627 Q6ZQ88
## 692858: 99982 22627 Q6ZQ88
## 692859: 99982 30841 Q6ZQ88
## 692860: 99982 71950 Q6ZQ88
## 692861: 99982 81879 Q6ZQ88
## IDs_interactor_A
## 1: A0A0H3K900
## 2: A5U0E5
## 3: A6MW92
## 4: A6TG64
## 5: A8DS38
## ---
## 692857: P62259
## 692858: P62259
## 692859: Q6P1G2
## 692860: Q80Z64
## 692861: Q3UNW5
## Alt._IDs_interactor_A
## 1: intact:EBI-2465150
## 2: intact:EBI-6409272
## 3: intact:EBI-1792769
## 4: intact:EBI-8066161|intact:MINT-8392347
## 5: intact:EBI-6995359|intact:MINT-8187004
## ---
## 692857: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692858: intact:EBI-356480|uniprotkb:P29360|uniprotkb:P42655|uniprotkb:Q63631
## 692859: intact:EBI-1216214|uniprotkb:Q3V396|uniprotkb:Q6PFD0|uniprotkb:Q6ZPE8|uniprotkb:Q9CSF7|uniprotkb:Q9QZN6
## 692860: intact:EBI-2312517|uniprotkb:Q6SMR1|uniprotkb:Q7TN85
## 692861: intact:EBI-5691372|uniprotkb:Q99PF2|uniprotkb:Q14AW3
## Alt._IDs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692858: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692859: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692860: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## 692861: intact:EBI-1216284|uniprotkb:Q6PB53|uniprotkb:Q8VEA1|uniprotkb:A3KG94
## Aliases_interactor_A
## 1: psi-mi:a0a0h3k900_staae(display_long)|uniprotkb:phoR(gene name)|psi-mi:phoR(display_short)|uniprotkb:NWMN_1585(locus name)
## 2: psi-mi:a5u0e5_mycta(display_long)|uniprotkb:phoP(gene name)|psi-mi:phoP(display_short)|uniprotkb:MRA_0767(locus name)
## 3: psi-mi:a6mw92_maize(display_long)|uniprotkb:bif2(gene name)|psi-mi:bif2(display_short)
## 4: psi-mi:a6tg64_klep7(display_long)|uniprotkb:Serine/threonine-protein kinase SrkA(gene name synonym)|uniprotkb:srkA(gene name synonym)|uniprotkb:KPN_04169(orf name)|uniprotkb:yihE(gene name)|psi-mi:yihE(display_short)
## 5: psi-mi:a8ds38_tabdi(display_long)
## ---
## 692857: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692858: psi-mi:1433e_mouse(display_long)|uniprotkb:Ywhae(gene name)|psi-mi:Ywhae(display_short)
## 692859: psi-mi:kdm2b_mouse(display_long)|uniprotkb:Kdm2b(gene name)|psi-mi:Kdm2b(display_short)|uniprotkb:Fbl10(gene name synonym)|uniprotkb:Jhdm1b(gene name synonym)|uniprotkb:Kiaa3014(gene name synonym)|uniprotkb:[Histone-H3]-lysine-36 demethylase 1B(gene name synonym)|uniprotkb:F-box and leucine-rich repeat protein 10(gene name synonym)|uniprotkb:F-box/LRR-repeat protein 10(gene name synonym)|uniprotkb:F-box protein FBL10(gene name synonym)|uniprotkb:Fbxl10(gene name synonym)|uniprotkb:JmjC domain-containing histone demethylation protein 1B(gene name synonym)
## 692860: psi-mi:nanog_mouse(display_long)|uniprotkb:Nanog(gene name)|psi-mi:Nanog(display_short)|uniprotkb:Ecat4(gene name synonym)|uniprotkb:Enk(gene name synonym)|uniprotkb:Homeobox transcription factor Nanog(gene name synonym)|uniprotkb:Early embryo specific expression NK-type homeobox protein(gene name synonym)|uniprotkb:ES cell-associated protein 4(gene name synonym)
## 692861: psi-mi:tf2l1_mouse(display_long)|uniprotkb:Tfcp2l1(gene name)|psi-mi:Tfcp2l1(display_short)|uniprotkb:CP2-related transcriptional repressor 1(gene name synonym)|uniprotkb:Crtr1(gene name synonym)|uniprotkb:Tcfcp2l1(gene name synonym)
## Aliases_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692858: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692859: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692860: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## 692861: psi-mi:kdm1a_mouse(display_long)|uniprotkb:Kdm1a(gene name)|psi-mi:Kdm1a(display_short)|uniprotkb:Kiaa0601(gene name synonym)|uniprotkb:Lsd1(gene name synonym)|uniprotkb:Flavin-containing amine oxidase domain-containing protein 2(gene name synonym)|uniprotkb:BRAF35-HDAC complex protein BHC110(gene name synonym)|uniprotkb:Aof2(gene name synonym)
## Interaction_detection_methods
## 1: psi-mi:"MI:0424"(protein kinase assay)
## 2: psi-mi:"MI:0030"(cross-linking study)
## 3: psi-mi:"MI:0424"(protein kinase assay)
## 4: psi-mi:"MI:0424"(protein kinase assay)
## 5: psi-mi:"MI:0435"(protease assay)
## ---
## 692857: psi-mi:"MI:0027"(cosedimentation)
## 692858: psi-mi:"MI:0027"(cosedimentation)
## 692859: psi-mi:"MI:0096"(pull down)
## 692860: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## 692861: psi-mi:"MI:0007"(anti tag coimmunoprecipitation)
## Publication_1st_authors Publication_Identifiers
## 1: Casino et al. (2009) 19800110
## 2: Gupta et al. (2009) 19820095
## 3: Skirpan et al. (2008) 18466309
## 4: Srinivasan et al. (2012) 23010593
## 5: Dutta et al. (2011) 21707922
## ---
## 692857: Kislinger et al. (2006) 16615898
## 692858: Kislinger et al. (2006) 16615898
## 692859: Sanchez et al. (2007) 17296600
## 692860: Gagliardi et al. (2013) 23892456
## 692861: van et al. (2010) 20362541
## Taxid_interactor_A Taxid_interactor_B
## 1: 426430 -
## 2: 419947 -
## 3: 4577 -
## 4: 272620 -
## 5: 52861 -
## ---
## 692857: 10090 10090
## 692858: 10090 10090
## 692859: 10090 10090
## 692860: 10090 10090
## 692861: 10090 10090
## Interaction_types
## 1: psi-mi:"MI:0217"(phosphorylation reaction)
## 2: psi-mi:"MI:0915"(physical association)
## 3: psi-mi:"MI:0217"(phosphorylation reaction)
## 4: psi-mi:"MI:0217"(phosphorylation reaction)
## 5: psi-mi:"MI:0194"(cleavage reaction)
## ---
## 692857: psi-mi:"MI:0403"(colocalization)
## 692858: psi-mi:"MI:0403"(colocalization)
## 692859: psi-mi:"MI:0914"(association)
## 692860: psi-mi:"MI:0914"(association)
## 692861: psi-mi:"MI:0914"(association)
## Source_databases Interaction_identifiers Confidence_values
## 1: psi-mi:"MI:0469"(IntAct) EBI-2465076 0.44
## 2: psi-mi:"MI:0903"(mpidb) EBI-6409277 0.40
## 3: psi-mi:"MI:0469"(IntAct) EBI-1792855 NA
## 4: psi-mi:"MI:0471"(MINT) EBI-8066173 NA
## 5: psi-mi:"MI:0471"(MINT) EBI-6995391 NA
## ---
## 692857: psi-mi:"MI:0471"(MINT) EBI-8412660 0.35
## 692858: psi-mi:"MI:0471"(MINT) EBI-8459929 0.35
## 692859: psi-mi:"MI:0469"(IntAct) EBI-1249446 0.35
## 692860: psi-mi:"MI:0471"(MINT) EBI-8820601 0.35
## 692861: psi-mi:"MI:0469"(IntAct) EBI-5735888 0.35
## Expansion_methods
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:1060"(spoke expansion)
## 692858: psi-mi:"MI:1060"(spoke expansion)
## 692859: psi-mi:"MI:1060"(spoke expansion)
## 692860: psi-mi:"MI:1060"(spoke expansion)
## 692861: psi-mi:"MI:1060"(spoke expansion)
## Biological_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0499"(unspecified role)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Biological_roles_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0499"(unspecified role)
## 692858: psi-mi:"MI:0499"(unspecified role)
## 692859: psi-mi:"MI:0499"(unspecified role)
## 692860: psi-mi:"MI:0499"(unspecified role)
## 692861: psi-mi:"MI:0499"(unspecified role)
## Experimental_roles_interactor_A
## 1: psi-mi:"MI:0503"(self)
## 2: psi-mi:"MI:0497"(neutral component)
## 3: psi-mi:"MI:0898"(putative self)
## 4: psi-mi:"MI:0503"(self)
## 5: psi-mi:"MI:0503"(self)
## ---
## 692857: psi-mi:"MI:0497"(neutral component)
## 692858: psi-mi:"MI:0497"(neutral component)
## 692859: psi-mi:"MI:0496"(bait)
## 692860: psi-mi:"MI:0496"(bait)
## 692861: psi-mi:"MI:0496"(bait)
## Experimental_roles_interactor_B Types_interactor_A
## 1: - psi-mi:"MI:0326"(protein)
## 2: - psi-mi:"MI:0326"(protein)
## 3: - psi-mi:"MI:0326"(protein)
## 4: - psi-mi:"MI:0326"(protein)
## 5: - psi-mi:"MI:0326"(protein)
## ---
## 692857: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0497"(neutral component) psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein)
## Types_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0326"(protein)
## 692858: psi-mi:"MI:0326"(protein)
## 692859: psi-mi:"MI:0326"(protein)
## 692860: psi-mi:"MI:0326"(protein)
## 692861: psi-mi:"MI:0326"(protein)
## Xrefs_interactor_A
## 1: go:"GO:0005524"(ATP binding)|refseq:WP_000975269.1|uniprotkb:A6QHM5(uniprot-removed-ac)|go:"GO:0000155"(phosphorelay sensor kinase activity)|go:"GO:0005622"(intracellular)|go:"GO:0016021"(integral component of membrane)|interpro:IPR000014(PAS)|interpro:IPR003594(ATP-binding region, ATPase-like)|interpro:IPR003660(Signal transduction histidine kinase, HAMP region)|interpro:IPR003661(Signal transduction histidine kinase, subgroup 1, dimerisation and phosphoacceptor region)|interpro:IPR004358(Signal transduction histidine kinase-related protein, C-terminal)|interpro:IPR005467(Signal transduction histidine kinase, core)
## 2: refseq:WP_012054162.1|go:"GO:0005622"(intracellular)|go:"GO:0006351"(transcription, DNA-templated)|interpro:IPR016032(Signal transduction response regulator, C-terminal effector)|go:"GO:0003677"(DNA binding)|go:"GO:0006355"(regulation of transcription, DNA-templated)|interpro:IPR001789(Signal transduction response regulator, receiver region)|interpro:IPR001867(Signal transduction response regulator, C-terminal)|interpro:IPR011006(CheY-like)|interpro:IPR011991(Winged helix repressor DNA-binding)|go:"GO:0000160"(phosphorelay signal transduction system)
## 3: go:"GO:0004672"(protein kinase activity)|interpro:IPR011009(Protein kinase-like)|interpro:IPR000719(Protein kinase, core)|interpro:IPR008271(Serine/threonine protein kinase, active site)|go:"GO:0005524"(ATP binding)|refseq:NP_001106051.1
## 4: interpro:IPR032882|interpro:IPR011009(Protein kinase-like)|interpro:IPR002575(Aminoglycoside phosphotransferase)|refseq:WP_004187940.1|go:"GO:0000287"(magnesium ion binding)|go:"GO:0004674"(protein serine/threonine kinase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005737"(cytoplasm)|go:"GO:0006950"(response to stress)|mint:MINT-8392362(identity)
## 5: interpro:IPR025661|interpro:IPR000169(Peptidase, cysteine peptidase active site)|interpro:IPR013201(Proteinase inhibitor I29, cathepsin propeptide)|interpro:IPR013128(Peptidase C1A, papain)|interpro:IPR000668(Peptidase C1A, papain C-terminal)|go:"GO:0008234"(cysteine-type peptidase activity)|rcsb pdb:2PRE|mint:MINT-8187033(identity)
## ---
## 692857: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428681(identity)
## 692858: ensembl:ENSMUSG00000020849|ensembl:ENSMUSP00000070993|ensembl:ENSMUST00000067664|go:"GO:0021762"(substantia nigra development)|go:"GO:0005739"(mitochondrion)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0021766"(hippocampus development)|go:"GO:0035308"(negative regulation of protein dephosphorylation)|go:"GO:0001764"(neuron migration)|go:"GO:0006605"(protein targeting)|refseq:NP_033562.3|interpro:IPR000308(14-3-3 protein)|interpro:IPR023409|interpro:IPR023410|go:"GO:0005871"(kinesin complex)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0005829"(cytosol)|go:"GO:0030659"(cytoplasmic vesicle membrane)|go:"GO:0005925"(focal adhesion)|go:"GO:0016020"(membrane)|go:"GO:0019899"(enzyme binding)|go:"GO:0023026"(MHC class II protein complex binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0044325"(ion channel binding)|go:"GO:0046982"(protein heterodimerization activity)|go:"GO:0050815"(phosphoserine binding)|go:"GO:0051219"(phosphoprotein binding)|go:"GO:0030424"(axon)|go:"GO:0042470"(melanosome)|reactome:R-MMU-8854518|go:"GO:0044822"("poly(A) RNA binding")|reactome:R-MMU-2565942|reactome:R-MMU-3371453|reactome:R-MMU-3371511|reactome:R-MMU-380259|reactome:R-MMU-380270|reactome:R-MMU-5620912|reactome:R-MMU-5625740|reactome:R-MMU-111447|reactome:R-MMU-5628897|reactome:R-MMU-1445148|reactome:R-MMU-75035|reactome:R-MMU-2028269|reactome:R-MMU-205025|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0015459"(potassium channel regulator activity)|go:"GO:0060306"(regulation of membrane repolarization)|go:"GO:0070062"(extracellular exosome)|go:"GO:1901016"(regulation of potassium ion transmembrane transporter activity)|go:"GO:1902309"(negative regulation of peptidyl-serine dephosphorylation)|go:"GO:0005737"(cytoplasm)|go:"GO:0005913"(cell-cell adherens junction)|go:"GO:0098641"(cadherin binding involved in cell-cell adhesion)|reactome:R-MMU-8876198|mint:MINT-4428693(identity)
## 692859: interpro:IPR032675|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0030307"(positive regulation of cell growth)|go:"GO:0070544"(histone H3-K36 demethylation)|go:"GO:1902459"(positive regulation of stem cell population maintenance)|reactome:R-MMU-3214842|go:"GO:0030900"(forebrain development)|go:"GO:0030902"(hindbrain development)|go:"GO:0031519"(PcG protein complex)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0035518"(histone H2A monoubiquitination)|go:"GO:0005730"(nucleolus)|ensembl:ENSMUST00000031435|ensembl:ENSMUST00000046073|ensembl:ENSMUSG00000029475|ensembl:ENSMUSP00000031435|ensembl:ENSMUSP00000038229|interpro:IPR006553(Leucine-rich repeat, cysteine-containing subtype)|refseq:NP_038938.1|interpro:IPR001810(Cyclin-like F-box)|interpro:IPR003347(Transcription factor jumonji/aspartyl beta-hydroxylase)|interpro:IPR002857(Zinc finger, CXXC-type)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR019787|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|go:"GO:0051864"("histone demethylase activity (H3-K36 specific)")|go:"GO:0019843"(rRNA binding)|go:"GO:0008270"(zinc ion binding)|go:"GO:0048596"(embryonic camera-type eye morphogenesis)|go:"GO:0021592"(fourth ventricle development)|go:"GO:0021993"(initiation of neural tube closure)|go:"GO:0021670"(lateral ventricle development)|go:"GO:0030901"(midbrain development)|go:"GO:0021555"(midbrain-hindbrain boundary morphogenesis)|go:"GO:2000178"(negative regulation of neural precursor cell proliferation)|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0007283"(spermatogenesis)|go:"GO:0021678"(third ventricle development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_001003953.1
## 692860: go:"GO:2000036"(regulation of stem cell population maintenance)|go:"GO:0009825"(multidimensional cell growth)|go:"GO:0036018"(cellular response to erythropoietin)|go:"GO:0042246"(tissue regeneration)|go:"GO:0072752"(cellular response to rapamycin)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0001714"(endodermal cell fate specification)|go:"GO:0005730"(nucleolus)|go:"GO:0008283"(cell proliferation)|go:"GO:0035019"(somatic stem cell population maintenance)|go:"GO:0003677"(DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0010033"(response to organic substance)|go:"GO:0010454"(negative regulation of cell fate commitment)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0045596"(negative regulation of cell differentiation)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0048863"(stem cell differentiation)|ensembl:ENSMUSP00000012540|ensembl:ENSMUSP00000108199|ensembl:ENSMUSP00000108200|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0010468"(regulation of gene expression)|go:"GO:0045595"(regulation of cell differentiation)|ensembl:ENSMUST00000012540|ensembl:ENSMUST00000112580|ensembl:ENSMUST00000112581|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0003682"(chromatin binding)|go:"GO:0001158"(enhancer sequence-specific DNA binding)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0009880"(embryonic pattern specification)|go:"GO:0008406"(gonad development)|go:"GO:0001710"(mesodermal cell fate commitment)|go:"GO:0030514"(negative regulation of BMP signaling pathway)|go:"GO:0042664"(negative regulation of endodermal cell fate specification)|go:"GO:0008284"(positive regulation of cell proliferation)|go:"GO:0045931"(positive regulation of mitotic cell cycle)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0032526"(response to retinoic acid)|go:"GO:0017145"(stem cell division)|go:"GO:0019827"(stem cell population maintenance)|refseq:XP_006506714.1|refseq:NP_082292.1|ensembl:ENSMUSG00000012396|interpro:IPR001356(Homeobox)|interpro:IPR017970|interpro:IPR009057(Homeodomain-like)|rcsb pdb:2VI6|refseq:NP_001276757.1|refseq:NP_001276759.1|refseq:NP_001276760.1|go:"GO:0006351"(transcription, DNA-templated)
## 692861: go:"GO:0016020"(membrane)|go:"GO:0000902"(cell morphogenesis)|go:"GO:0007028"(cytoplasm organization)|go:"GO:0008340"(determination of adult lifespan)|go:"GO:0002070"(epithelial cell maturation)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0045927"(positive regulation of growth)|go:"GO:0007431"(salivary gland development)|go:"GO:0006351"(transcription, DNA-templated)|refseq:NP_076244.2|interpro:IPR007604(CP2 transcription factor)|interpro:IPR013761(Sterile alpha motif-type)|go:"GO:0005667"(transcription factor complex)|go:"GO:0005737"(cytoplasm)|go:"GO:0005634"(nucleus)|ensembl:ENSMUST00000027629|ensembl:ENSMUSG00000026380|ensembl:ENSMUSP00000027629|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0043565"(sequence-specific DNA binding)
## Xrefs_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450494(identity)
## 692858: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)|mint:MINT-4450497(identity)
## 692859: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692860: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## 692861: go:"GO:0010569"(regulation of double-strand break repair via homologous recombination)|go:"GO:0033184"(positive regulation of histone ubiquitination)|go:"GO:0034644"(cellular response to UV)|go:"GO:0043234"(protein complex)|go:"GO:0071480"(cellular response to gamma radiation)|go:"GO:1903827"(regulation of cellular protein localization)|go:"GO:1990391"(DNA repair complex)|interpro:IPR023753|go:"GO:0005654"(nucleoplasm)|go:"GO:1903758"(negative regulation of transcription from RNA polymerase II promoter by histone modification)|reactome:R-MMU-3214842|reactome:R-MMU-5625886|go:"GO:0001085"(RNA polymerase II transcription factor binding)|go:"GO:0005634"(nucleus)|go:"GO:0006357"(regulation of transcription from RNA polymerase II promoter)|go:"GO:0008134"(transcription factor binding)|go:"GO:0000790"(nuclear chromatin)|go:"GO:0005667"(transcription factor complex)|go:"GO:0003682"(chromatin binding)|go:"GO:0050660"(flavin adenine dinucleotide binding)|go:"GO:0034648"("histone demethylase activity (H3-dimethyl-K4 specific)")|go:"GO:0032454"("histone demethylase activity (H3-K9 specific)")|go:"GO:0030374"(ligand-dependent nuclear receptor transcription coactivator activity)|go:"GO:0016491"(oxidoreductase activity)|go:"GO:0003700"(transcription factor activity, sequence-specific DNA binding)|go:"GO:0044212"(transcription regulatory region DNA binding)|go:"GO:0008283"(cell proliferation)|go:"GO:0030851"(granulocyte differentiation)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0055001"(muscle cell development)|interpro:IPR017366(Histone lysine-specific demethylase)|go:"GO:0043433"(negative regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:0000122"(negative regulation of transcription from RNA polymerase II promoter)|go:"GO:0021983"(pituitary gland development)|go:"GO:0045648"(positive regulation of erythrocyte differentiation)|go:"GO:0046886"(positive regulation of hormone biosynthetic process)|go:"GO:0045654"(positive regulation of megakaryocyte differentiation)|go:"GO:0045944"(positive regulation of transcription from RNA polymerase II promoter)|go:"GO:0010725"(regulation of primitive erythrocyte differentiation)|refseq:NP_598633.2|interpro:IPR002937(Amine oxidase)|go:"GO:0006351"(transcription, DNA-templated)|go:"GO:0050681"(androgen receptor binding)|go:"GO:0019899"(enzyme binding)|go:"GO:0032452"(histone demethylase activity)|go:"GO:0032453"("histone demethylase activity (H3-K4 specific)")|go:"GO:0033169"(histone H3-K9 demethylation)|go:"GO:0034720"(histone H3-K4 demethylation)|go:"GO:0043426"(MRF binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR009057(Homeodomain-like)|interpro:IPR007526(SWIRM)|interpro:IPR011991(Winged helix repressor DNA-binding)|ensembl:ENSMUST00000116273|ensembl:ENSMUSG00000036940|ensembl:ENSMUSP00000111977|go:"GO:0002039"(p53 binding)|go:"GO:0006482"(protein demethylation)|go:"GO:0032451"(demethylase activity)|go:"GO:0050767"(regulation of neurogenesis)|go:"GO:0050768"(negative regulation of neurogenesis)|go:"GO:1990138"(neuron projection extension)|go:"GO:0032091"(negative regulation of protein binding)|go:"GO:0043518"(negative regulation of DNA damage response, signal transduction by p53 class mediator)|go:"GO:0051091"(positive regulation of sequence-specific DNA binding transcription factor activity)|go:"GO:1902166"(negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator)|go:"GO:0051572"(negative regulation of histone H3-K4 methylation)|go:"GO:0051573"(negative regulation of histone H3-K9 methylation)|go:"GO:2000179"(positive regulation of neural precursor cell proliferation)|go:"GO:2000648"(positive regulation of stem cell proliferation)|go:"GO:0000784"(nuclear chromosome, telomeric region)|go:"GO:0042162"(telomeric DNA binding)|go:"GO:0061752"(telomeric repeat-containing RNA binding)|go:"GO:0000380"(alternative mRNA splicing, via spliceosome)|go:"GO:0010976"(positive regulation of neuron projection development)|go:"GO:0021987"(cerebral cortex development)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042551"(neuron maturation)|go:"GO:0045793"(positive regulation of cell size)|go:"GO:0046098"(guanine metabolic process)|go:"GO:0060992"(response to fungicide)|go:"GO:0071320"(cellular response to cAMP)
## Interaction_Xrefs
## 1: go:"GO:0046777"(protein autophosphorylation)|go:"GO:0004672"(protein kinase activity)
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: go:"GO:0005634"(nucleus)
## 692858: go:"GO:0005634"(nucleus)
## 692859: go:"GO:0005634"(nucleus)
## 692860: go:"GO:0005634"(nucleus)
## 692861: -
## Annotations_interactor_A Annotations_interactor_B
## 1: - -
## 2: - -
## 3: - -
## 4: comment:mint -
## 5: comment:mint -
## ---
## 692857: spectral count:7 spectral count:5
## 692858: spectral count:9 spectral count:9
## 692859: - -
## 692860: - -
## 692861: - -
## Interaction_annotations
## 1: figure legend:Fig. 5F|full coverage:Only protein-protein interactions|curation depth:imex curation
## 2: figure legend:Fig. 5|full coverage:Only protein-protein interactions|curation depth:imex curation
## 3: figure legend:Figure 3|comment:Bif2 was shown to autophosphorylate.
## 4: figure legend:f1|comment:mint|intra-molecular:true
## 5: figure legend:sf1|comment:mint|intra-molecular:true
## ---
## 692857: figure legend:ST1|comment:mint
## 692858: figure legend:ST1|comment:mint
## 692859: figure legend:4A|dataset:Apoptosis - Interactions involving proteins with a function related to apoptosis|dataset:Chromatin - Epigenetic interactions resulting in chromatin modulation
## 692860: figure legend:t1 st1|full coverage:Only protein-protein interactions|curation depth:imex curation
## 692861: figure legend:Supplementary Table 4 + 8, Figure 2D.|full coverage:Only protein-protein interactions|curation depth:imex curation
## Host_organisms Interaction_parameters Creation_date Update_date
## 1: -1 - 2009/10/21 2014/10/16
## 2: -1 - 2012/11/30 2014/10/16
## 3: -1 - 2008/07/16 2014/10/16
## 4: -1 - 2012/09/10 2014/10/16
## 5: -1 - 2011/06/14 2014/10/16
## ---
## 692857: 10090 - 2007/03/13 2016/11/30
## 692858: 10090 - 2007/03/13 2016/11/30
## 692859: 10090 - 2007/03/21 2014/10/16
## 692860: 10090 - 2013/10/23 2014/10/16
## 692861: 10090 - 2012/02/29 2014/10/16
## Checksums_interactor_A
## 1: rogid:f1Y/+UDZ3WsP2yvsjJf94FntkZw426430
## 2: rogid:1SwukqEqW/H9T6naynkr9SAdtj4419947
## 3: rogid:oMrfj4TfaFdtkKv98ZNc7fCadrI4577
## 4: rogid:WfbB1DvDuvtchMuIkV17/YdCVlQ272620
## 5: rogid:6LtDcYFGc5XYs1zKx1uXRn4gZJs52861
## ---
## 692857: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692858: rogid:mnuAjdnQZbMFojll2PnV3xFklXQ10090
## 692859: rogid:bNAPO2wQNjeaKjHXp02ErpRfSDw10090
## 692860: rogid:v8TDhd7PZnOKFS3djxouMHxftPs10090
## 692861: rogid:QtzNiWQU27XK2s0idF91/IAVi0E10090
## Checksums_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692858: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692859: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692860: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## 692861: rogid:4rlXgUzLs3mhV2FLX207Io9etU010090
## Interaction_Checksums
## 1: intact-crc:7BBA0D1EA237FEC3
## 2: intact-crc:4096C84569EA780A
## 3: intact-crc:388A04F50F31D812
## 4: intact-crc:0313C9ADE7ADCCCC
## 5: intact-crc:40C3AD7BE9F4C193
## ---
## 692857: intact-crc:A16CFA73CF6AE082
## 692858: intact-crc:1B66D582CA1FAD01
## 692859: intact-crc:75642DE2B905DD44|rigid:W0bsCwxpYX8+OuDZDxj7QMajzgM
## 692860: intact-crc:B3ED58BF30D17C05|rigid:b8XXlh+d4ezd3xoFuCzS1wEcnOs
## 692861: intact-crc:8889A2183786C4BC|rigid:qPM+mcj1rQf5up/kjdxdiC3xoHo
## Negative
## 1: false
## 2: false
## 3: false
## 4: false
## 5: false
## ---
## 692857: false
## 692858: false
## 692859: false
## 692860: false
## 692861: false
## Features_interactor_A
## 1: sufficient binding region:316-554(IPR005467)
## 2: his tag:n-n|mutation increasing interaction strength:21-21
## 3: glutathione s tranferase tag:?-?|mutation disrupting interaction:161-161|mutation disrupting interaction:258-258
## 4: -
## 5: his tag:?-?(MINT-8187036)
## ---
## 692857: -
## 692858: -
## 692859: fusion protein:n-n|biotin tag:n-n
## 692860: flag tag:?-?
## 692861: flag tag:c-c
## Features_interactor_B Stoichiometrys_interactor_A
## 1: - -
## 2: - 1
## 3: - -
## 4: - -
## 5: - -
## ---
## 692857: - -
## 692858: - -
## 692859: - -
## 692860: - -
## 692861: - -
## Stoichiometrys_interactor_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: -
## 692858: -
## 692859: -
## 692860: -
## 692861: -
## Identification_method_participant_A
## 1: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 2: psi-mi:"MI:0396"(predetermined participant)
## 3: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 4: psi-mi:"MI:0821"(molecular weight estimation by autoradiography)
## 5: psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## Identification_method_participant_B
## 1: -
## 2: -
## 3: -
## 4: -
## 5: -
## ---
## 692857: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692858: psi-mi:"MI:0427"(Identification by mass spectrometry)
## 692859: psi-mi:"MI:0113"(western blot)
## 692860: psi-mi:"MI:0032"(de novo protein sequencing by mass spectrometry)
## 692861: psi-mi:"MI:0102"(sequence tag identification)
## interactor_IDs_databases_A interactor_IDs_databases_B
## 1: uniprotkb -
## 2: uniprotkb -
## 3: uniprotkb -
## 4: uniprotkb -
## 5: uniprotkb -
## ---
## 692857: uniprotkb uniprotkb
## 692858: uniprotkb uniprotkb
## 692859: uniprotkb uniprotkb
## 692860: uniprotkb uniprotkb
## 692861: uniprotkb uniprotkb
## bait_prey_status_A bait_prey_status_B IDs_interactor_A_isoforms
## 1: self - A0A0H3K900
## 2: neutral component - A5U0E5
## 3: putative self - A6MW92
## 4: self - A6TG64
## 5: self - A8DS38
## ---
## 692857: neutral component neutral component P62259
## 692858: neutral component neutral component P62259
## 692859: bait prey Q6P1G2
## 692860: bait prey Q80Z64
## 692861: bait prey Q3UNW5
## IDs_interactor_B_isoforms interactor_A_total_PMID
## 1: - NA
## 2: - NA
## 3: - NA
## 4: - NA
## 5: - NA
## ---
## 692857: Q6ZQ88 95
## 692858: Q6ZQ88 95
## 692859: Q6ZQ88 49
## 692860: Q6ZQ88 332
## 692861: Q6ZQ88 39
## interactor_B_total_PMID unique_interactions
## 1: NA -_A0A0H3K900
## 2: NA -_A5U0E5
## 3: NA -_A6MW92
## 4: NA -_A6TG64
## 5: NA -_A8DS38
## ---
## 692857: 103 P62259_Q6ZQ88
## 692858: 103 P62259_Q6ZQ88
## 692859: 103 Q6P1G2_Q6ZQ88
## 692860: 103 Q6ZQ88_Q80Z64
## 692861: 103 Q3UNW5_Q6ZQ88
## unique_interactions_per_Publication
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: 6557
## 692858: 6557
## 692859: 61
## 692860: 137
## 692861: 282
## interaction_ids_per_Publication
## 1: 9
## 2: 3
## 3: 6
## 4: 1
## 5: 2
## ---
## 692857: 24
## 692858: 24
## 692859: 10
## 692860: 12
## 692861: 60
## unique_interactions_per_Publication_nospoke
## 1: 6
## 2: 2
## 3: 2
## 4: 1
## 5: 2
## ---
## 692857: NA
## 692858: NA
## 692859: NA
## 692860: NA
## 692861: NA
## interaction_ids_per_Publication_nospoke large_scale small_scale
## 1: 9 0 1
## 2: 3 0 1
## 3: 6 0 1
## 4: 1 0 1
## 5: 2 0 1
## ---
## 692857: NA 0 1
## 692858: NA 0 1
## 692859: NA 0 1
## 692860: NA 0 1
## 692861: NA 0 1
## unique_interactions_isoforms unique_interactions_per_interactor_A
## 1: -_A0A0H3K900 2
## 2: -_A5U0E5 2
## 3: -_A6MW92 2
## 4: -_A6TG64 1
## 5: -_A8DS38 2
## ---
## 692857: P62259_Q6ZQ88 4025
## 692858: P62259_Q6ZQ88 4025
## 692859: Q6P1G2_Q6ZQ88 11
## 692860: Q6ZQ88_Q80Z64 153
## 692861: Q3UNW5_Q6ZQ88 143
## unique_interactions_per_interactor_B
## 1: 174
## 2: 174
## 3: 174
## 4: 174
## 5: 174
## ---
## 692857: 7
## 692858: 7
## 692859: 7
## 692860: 7
## 692861: 7# interactions to proteins and genes
## tagging interactors by the scale of the study
{
all.IntAct.proteins_scale_l = all.IntAct.modif[,data.table(
IDs_interactor = c(IDs_interactor_A,IDs_interactor_B),
large_scale = c(large_scale, large_scale))]
all.IntAct.proteins_scale_s = all.IntAct.modif[,data.table(
IDs_interactor = c(IDs_interactor_A,IDs_interactor_B),
small_scale = c(small_scale, small_scale))]
all.IntAct.proteins_scale_l = unique(all.IntAct.proteins_scale_l)
all.IntAct.proteins_scale_s = unique(all.IntAct.proteins_scale_s)
all.IntAct.proteins_scale = merge(all.IntAct.proteins_scale_l,all.IntAct.proteins_scale_s, by.x = "IDs_interactor", by.y = "IDs_interactor",all = T)
all.IntAct.proteins_scale[,large_small_scale := paste0(large_scale,".",small_scale)]
all.IntAct.proteins_scale = all.IntAct.proteins_scale[!(small_scale ==0 & large_scale ==0), ]
all.IntAct.proteins_scale = unique(all.IntAct.proteins_scale)
}
# Calculating aggregated MI score per GeneID (includes interactions between proteins encoded by that gene)
{
all.IntAct.proteins.score = all.IntAct.modif[,data.table(
IDs_interactor = c(IDs_interactor_A,IDs_interactor_B),
Confidence_values = as.numeric(c(Confidence_values,Confidence_values)),
interactor_GeneID = c(IDs_interactor_A_GeneID, IDs_interactor_B_GeneID))]
all.IntAct.proteins.score = unique(all.IntAct.proteins.score)
all.IntAct.proteins.score[,Median_MI_score := median(Confidence_values, na.rm = T), by = interactor_GeneID]
all.IntAct.proteins.score[,Mean_MI_score := mean(Confidence_values, na.rm = T), by = interactor_GeneID]
all.IntAct.proteins.score[,sum_MI_score := sum(Confidence_values, na.rm = T), by = interactor_GeneID]
all.IntAct.proteins.score[,Confidence_values := NULL]
all.IntAct.proteins.score = unique(all.IntAct.proteins.score)
}
# merging the number of interactions, the scale of the study, and the MIscore tables
{
all.IntAct.proteins = all.IntAct.modif[,data.table(
IDs_interactor = c(IDs_interactor_A,IDs_interactor_B),
interactor_total_PMID = c(interactor_A_total_PMID,interactor_B_total_PMID),
Taxid_interactor = c(Taxid_interactor_A,Taxid_interactor_B),
interactor_IDs_databases = c(interactor_IDs_databases_A, interactor_IDs_databases_B),
unique_interactions_per_interactor = c(unique_interactions_per_interactor_A, unique_interactions_per_interactor_B)
)]
all.IntAct.proteins = unique(all.IntAct.proteins)
all.IntAct.proteins = merge(all.IntAct.proteins,all.IntAct.proteins_scale, by.x = "IDs_interactor", by.y = "IDs_interactor",all = T)
all.IntAct.proteins= unique(all.IntAct.proteins)
all.IntAct.proteins = merge(all.IntAct.proteins,all.IntAct.proteins.score, by.x = "IDs_interactor", by.y = "IDs_interactor",all = T)
all.IntAct.proteins= unique(all.IntAct.proteins)
str(all.IntAct.proteins)
}## Classes 'data.table' and 'data.frame': 190119 obs. of 12 variables:
## $ IDs_interactor : chr "-" "-" "-" "000035833\"" ...
## $ interactor_total_PMID : int NA NA NA NA NA NA NA NA NA NA ...
## $ Taxid_interactor : chr "-" "-" "-" "9606" ...
## $ interactor_IDs_databases : chr "-" "-" "-" "protein ontology" ...
## $ unique_interactions_per_interactor: int 174 174 174 1 2 2 1 1 4 6 ...
## $ large_scale : num 0 1 1 0 0 0 0 1 0 0 ...
## $ small_scale : num 1 1 0 1 1 1 1 0 1 1 ...
## $ large_small_scale : chr "0.1" "1.1" "1.0" "0.1" ...
## $ interactor_GeneID : chr NA NA NA NA ...
## $ Median_MI_score : num 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 ...
## $ Mean_MI_score : num 0.414 0.414 0.414 0.414 0.414 ...
## $ sum_MI_score : num 10677 10677 10677 10677 10677 ...
## - attr(*, ".internal.selfref")=<externalptr>
## - attr(*, "sorted")= chr "IDs_interactor"{
# Select only relevant species, only uniprotkb identifiers,
all.IntAct.proteins = all.IntAct.proteins[Taxid_interactor %in% SPECIES_IDs & interactor_IDs_databases == "uniprotkb",]
# filter out proteins not mapped to geneID
all.IntAct.proteins = all.IntAct.proteins[,n_geneid := as.numeric(length(unique(interactor_GeneID))),by = IDs_interactor]
# filter out genes without proteins mapped to them - NA
all.IntAct.proteins = all.IntAct.proteins[,n_protid := as.numeric(length(unique(IDs_interactor))),by = interactor_GeneID][n_protid < max(n_protid),]
# tag proteins by the number of mappings - one_to_one or one_to_many
all.IntAct.proteins = all.IntAct.proteins[n_geneid > 1 | n_protid > 1, gene_id_prot_id := "one_to_many"]
# filter out genes without proteins mapped to them - NA
all.IntAct.proteins = all.IntAct.proteins[n_geneid == 1 & n_protid == 1, gene_id_prot_id := "one_to_one"]
SPECIES_NAME_ID = data.table(SPECIES_ID = SPECIES_IDs, SPECIES_NAME = SPECIES_NAME)
all.IntAct.proteins = merge(all.IntAct.proteins, SPECIES_NAME_ID, by.x = "Taxid_interactor", by.y = "SPECIES_ID", all=TRUE)
all.IntAct.proteins = all.IntAct.proteins[complete.cases(all.IntAct.proteins),]
str(all.IntAct.proteins)
}## Classes 'data.table' and 'data.frame': 133976 obs. of 16 variables:
## $ Taxid_interactor : chr "10090" "10090" "10090" "10090" ...
## $ IDs_interactor : chr "A0A023T778" "A0A0A0MQ89" "A0A0B4J1F4" "A0A0G2JDV6" ...
## $ interactor_total_PMID : int 17 13 16 27 69 16 16 81 42 44 ...
## $ interactor_IDs_databases : chr "uniprotkb" "uniprotkb" "uniprotkb" "uniprotkb" ...
## $ unique_interactions_per_interactor: int 1 1 1 1 1 14 5 3 2 2 ...
## $ large_scale : num 0 0 1 0 0 0 0 0 0 0 ...
## $ small_scale : num 1 1 0 1 1 1 1 1 1 1 ...
## $ large_small_scale : chr "0.1" "0.1" "1.0" "0.1" ...
## $ interactor_GeneID : chr "66441" "109275" "66412" "74383" ...
## $ Median_MI_score : num 0.35 0.35 0.35 0.35 0.35 0.435 0.435 0.36 0.35 0.375 ...
## $ Mean_MI_score : num 0.35 0.35 0.35 0.35 0.35 ...
## $ sum_MI_score : num 0.35 0.35 0.35 1.05 0.7 2.72 2.72 1.6 1.1 0.75 ...
## $ n_geneid : num 1 1 1 1 1 1 1 1 1 1 ...
## $ n_protid : num 1 1 1 3 2 1 1 2 2 1 ...
## $ gene_id_prot_id : chr "one_to_one" "one_to_one" "one_to_one" "one_to_many" ...
## $ SPECIES_NAME : chr "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" ...
## - attr(*, "sorted")= chr "Taxid_interactor"
## - attr(*, ".internal.selfref")=<externalptr>plot((all.IntAct.proteins$Median_MI_score),(all.IntAct.proteins$Mean_MI_score), main = "Median_MI_score vs Mean_MI_score")
# how many geneID per protein?
all.IntAct.proteins[,table(n_geneid,useNA = "ifany")]## n_geneid
## 1 2 3 4 5 6 7 8 9 10
## 125050 3048 552 272 160 246 56 336 72 420
## 13 14 15 16 17 23
## 507 1176 75 80 408 1518all.IntAct.proteins[,table(n_protid,useNA = "ifany")]## n_protid
## 1 2 3 4 5 6
## 123740 9154 841 133 77 31mean(all.IntAct.modif[,is.na(Confidence_values)])## [1] 0.158101mean(all.IntAct.proteins[,is.na(Median_MI_score)])## [1] 0library(MASS)
# plotting Median_MI_score as a function of the number of publications
library(ggplot2)
{
ggplot(all.IntAct.proteins, aes(interactor_total_PMID, Median_MI_score))+ scale_x_log10() +
#geom_density_2d(bins = 15,aes(colour=..level..)) +
#scale_color_gradient(low = "grey", high = "black")+
ggtitle("The relationship between the number of publications per gene and median MI score", subtitle = "line was fitted using robust linear regression, mapping of geneID to UniprotAC")+
ylab("median MI score for the interactions \n including the proteins encoded by that gene") + xlab("the number of publications per gene") + geom_smooth(method = "rlm", se = T) +ylim(0,1)+
facet_grid(SPECIES_NAME~gene_id_prot_id) + geom_point(size = 0.1, alpha = 0.05)+
theme(strip.text.y = element_text(angle = 0))
}
{
ggplot(all.IntAct.proteins, aes(interactor_total_PMID, sum_MI_score))+ scale_x_log10() +
#geom_density_2d(bins = 15,aes(colour=..level..)) +
#scale_color_gradient(low = "grey", high = "black")+
ggtitle("The relationship between the number of publications per gene and the sum of MI scores", subtitle = "line was fitted using robust linear regression, large and small scale experiments")+
ylab("the sum of MI scores for the interactions \n including the proteins encoded by that gene") + xlab("the number of publications per gene") + geom_smooth(method = "rlm", se = T) +ylim(0,all.IntAct.proteins[,max(sum_MI_score)])+
facet_grid(SPECIES_NAME~large_small_scale) + geom_point(size = 0.1, alpha = 0.05)+
theme(strip.text.y = element_text(angle = 0))
}## Warning: Removed 124 rows containing missing values (geom_smooth).
# plotting Median_MI_score as a function of the number of publications and the scale of the study
{
ggplot(all.IntAct.proteins, aes(interactor_total_PMID, Median_MI_score))+ scale_x_log10() + #geom_density_2d(bins = 30,aes(colour=..level..)) +
#scale_color_gradient(low = "grey", high = "black", breaks=c(0,10,50,100,200,500))+
ggtitle("The relationship between the number of publications per gene and median MI score", subtitle = "line was fitted using robust linear regression, large and small scale experiments")+
ylab("median MI score for the interactions \n including the proteins encoded by that gene") + xlab("the number of publications per gene") + geom_smooth(method = "rlm", se = T) +geom_point(size = 0.1, alpha = 0.05)+ylim(0,1)+
facet_grid(SPECIES_NAME ~ large_small_scale) +
theme(strip.text.y = element_text(angle = 0))
}## Warning in rlm.default(x, y, weights, method = method, wt.method =
## wt.method, : 'rlm' failed to converge in 20 steps
# plotting unique_interactions_per_interactor as a function of the number of publications
{
ggplot(all.IntAct.proteins, aes(interactor_total_PMID, unique_interactions_per_interactor))+
geom_density_2d(bins = 30,aes(colour=..level..)) + scale_x_log10()+ scale_y_log10() +
scale_color_gradient(low = "grey", high = "black", breaks=c(0,10,50,100,200,500))+
ggtitle("The relationship between the number of publications per gene and \n the number of interactions in which proteins encoded by that gene participate", subtitle = "line was fitted using robust linear regression, \n all UniprotAC were coerced to generic UniprotAC, \n mapping of geneID to UniprotAC")+
ylab("the number of interactions(per protein) in which proteins encoded by that gene participate") + xlab("the number of publications per gene") +
geom_smooth(method = "rlm", se = T)+
facet_grid(SPECIES_NAME~gene_id_prot_id, scales = "free") + geom_point(size = 0.1, alpha = 0.05)+
theme(strip.text.y = element_text(angle = 0))
}
{
ggplot(all.IntAct.proteins, aes(interactor_total_PMID, unique_interactions_per_interactor))+
geom_density_2d(bins = 30,aes(colour=..level..)) + scale_x_log10()+ scale_y_log10() +
scale_color_gradient(low = "grey", high = "black", breaks=c(0,10,50,100,200,500))+
ggtitle("The relationship between the number of publications per gene and \n the number of interactions in which proteins encoded by that gene participate", subtitle = "line was fitted using robust linear regression, \n all UniprotAC were coerced to generic UniprotAC, \n large and small scale experiments")+
ylab("the number of interactions(per protein) in which proteins encoded by that gene participate") + xlab("the number of publications per gene") +
geom_smooth(method = "rlm", se = T)+
facet_grid(SPECIES_NAME~large_small_scale, scales = "free") + geom_point(size = 1, alpha = 0.1)+
theme(strip.text.y = element_text(angle = 0))
}
# read the saved table with human_not_in_IMEx_protein_properties_processing chunk
SPECIES_NAME = c("Homo sapiens", "Mus musculus", "strain ATCC 204508", "strain K12")
## only reviewed = 2 and isoforms = FALSE is relevant for this analysis
reviewed = 2
isoforms = FALSE
##============================================================================##
source("SPECIES_NAME_TO_ID.R")
proteome_vs_imex_interaction_details_all = data.table()
library(dplyr)## -------------------------------------------------------------------------## data.table + dplyr code now lives in dtplyr.
## Please library(dtplyr)!## -------------------------------------------------------------------------##
## Attaching package: 'dplyr'## The following object is masked from 'package:MASS':
##
## select## The following objects are masked from 'package:data.table':
##
## between, first, last## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionfor (r in reviewed) {
for (i in isoforms) {
for (n in SPECIES_NAME) {
SPECIES_IDs = SPECIES_NAME_TO_ID(n)
SPECIES_ID = SPECIES_IDs$SPECIES_ID
filename = paste("./analysis/","proteome_vs_interactome_interaction_properties_f_", n,"_reviewed_",r,"_isoforms_",i,"_", date,".txt", sep = "")
proteome_vs_imex_interaction_details_f = as.data.table(read.delim(filename, header = T, stringsAsFactors = F,quote=""))
n = gsub("strain ATCC 204508", "S. cerevisiae, strain S288c", n)
n = gsub("strain K12", "Escherichia coli, strain K12", n)
proteome_vs_imex_interaction_details_f[ , c("SPECIES_NAME","reviewed","isoforms", "SPECIES_ID") := list(n,r,i,SPECIES_ID)]
proteome_vs_imex_interaction_details_all = rbind(proteome_vs_imex_interaction_details_all,proteome_vs_imex_interaction_details_f, fill =T)
}}}## [1] "UP000005640 9606 HUMAN 21032 71899 93381 Homo sapiens (Human)"
## Proteome_ID SPECIES_ID
## 1 UP000005640 9606
## [1] "UP000000589 10090 MOUSE 22280 36150 58884 Mus musculus (Mouse)"
## Proteome_ID SPECIES_ID
## 1 UP000000589 10090
## [1] "UP000002311 559292 YEAST 6721 31 6760 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)"
## Proteome_ID SPECIES_ID
## 1 UP000002311 559292
## [1] "UP000000625 83333 ECOLI 4306 9 8436 Escherichia coli (strain K12)"
## [2] "UP000002185 75379 THIK1 3134 0 3172 Thiomonas intermedia (strain K12) (Thiobacillus intermedius)"
## Proteome_ID SPECIES_ID
## 1 UP000000625 83333all.IntAct.protein_interaction_details_all = merge(x = proteome_vs_imex_interaction_details_all, y=all.IntAct.proteins, by.x = "whole_proteome_IDs", by.y = "IDs_interactor", nomatch=0)
all.IntAct.protein_interaction_details_all = all.IntAct.protein_interaction_details_all[two_hybrid_vs_AP_MS != "not in IMEx" & SPECIES_NAME.x %in% c("Homo sapiens", "Mus musculus", "S. cerevisiae, strain S288c", "Escherichia coli, strain K12"),]
{
ggplot(all.IntAct.protein_interaction_details_all, aes(interactor_total_PMID, unique_interactions_per_interactor, color = two_hybrid_vs_AP_MS))+
scale_x_log10()+ scale_y_log10() +
ggtitle("The relationship between the number of publications per gene and \n the number of interactions in which proteins encoded by that gene participate", subtitle = "line was fitted using robust linear regression, \n all UniprotAC were coerced to generic UniprotAC, \n large and small scale experiments")+
ylab("the number of interactions(per protein) in which proteins encoded by that gene participate") + xlab("the number of publications per gene") +
geom_smooth(method = "rlm", se = T)+
facet_grid(SPECIES_NAME.x~large_small_scale, scales = "free") + geom_point(size = 0.5, alpha = 0.1)+
theme(strip.text.y = element_text(angle = 0))
}
print(all.IntAct.protein_interaction_details_all[,table(SPECIES_NAME.x,large_small_scale, two_hybrid_vs_AP_MS)])## , , two_hybrid_vs_AP_MS = not two-hybrid, and not AP-MS
##
## large_small_scale
## SPECIES_NAME.x 0.1 1.0 1.1
## Escherichia coli, strain K12 361 1816 253
## Homo sapiens 963 775 272
## Mus musculus 3643 50 33
## S. cerevisiae, strain S288c 226 475 78
##
## , , two_hybrid_vs_AP_MS = not two-hybrid, AP-MS
##
## large_small_scale
## SPECIES_NAME.x 0.1 1.0 1.1
## Escherichia coli, strain K12 251 562 236
## Homo sapiens 2166 2220 1696
## Mus musculus 3213 923 732
## S. cerevisiae, strain S288c 671 947 605
##
## , , two_hybrid_vs_AP_MS = two-hybrid and AP-MS
##
## large_small_scale
## SPECIES_NAME.x 0.1 1.0 1.1
## Escherichia coli, strain K12 418 754 416
## Homo sapiens 12033 13438 11965
## Mus musculus 1011 729 704
## S. cerevisiae, strain S288c 4490 5896 4490
##
## , , two_hybrid_vs_AP_MS = two-hybrid, not AP-MS
##
## large_small_scale
## SPECIES_NAME.x 0.1 1.0 1.1
## Escherichia coli, strain K12 394 1642 340
## Homo sapiens 2784 6841 2534
## Mus musculus 1246 696 500
## S. cerevisiae, strain S288c 759 2397 752